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  • 92
    Celera contig
    Sources of linking information between <t>contigs.</t> ( A ) overlaps, ( B ) clone mates, ( C ) alignments to reference genome, ( D ) alignments to physical maps, ( E ) conservation of gene synteny.
    Contig, supplied by Celera, used in various techniques. Bioz Stars score: 92/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc contig
    Comparison of transcription levels estimation. A . Scaterplot of the number of 454 <t>FLX</t> reads used in the assembly of a given <t>contig</t> versus the number of Illumina reads mapping on the same contig. R1 and R2 stand for the correlation coefficients before and after disregarding the points that exhibit an extreme discrepancy between the two technologies (those ones forming an almost vertical line on the rightmost part of the figure). B . This figure depicts a depth profile showing the reads that map on a given genomic region. The upper part corresponds to 454 FLX, Illumina reads appear in the middle and the last part corresponds to the graphical representation of the corresponding genomic region.
    Contig, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 531 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    SourceForge net contig
    Targeted assembly of secondary metabolite synthesizing protein families from the in vitro human oral biofilm MT data set. Only the protein <t>contigs</t> longer than 60aa and nucleotide contigs longer than 180nt were considered. (A) Normalized N50 for protein assembly. (B) Normalized N50 for nucleotide assembly. For (A) and (B), red color indicates the performance of HMMER3 and blue color indicates HMM-GRASPx. The x-axes indicate assembly cases and were sorted based on the decreasing values of the HMMER3 performance and then the decreasing values of the HMM-GRASPx performance. Assembly cases without corresponding red bars indicate that no contig was assembled using HMMER3 predictions. (C) Log2 fold change for the N50 measures in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction. (D) Log2 fold change for the number of assembled reads in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction.
    Contig, supplied by SourceForge net, used in various techniques. Bioz Stars score: 92/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Unigene contig
    Distributions of ESTs in Contigs . Assembly of 12,084 ESTs resulted in <t>2258</t> contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each <t>contig</t> was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.
    Contig, supplied by Unigene, used in various techniques. Bioz Stars score: 92/100, based on 132 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Pacific Biosciences contigs
    Comparisons of the assemblers conducted in this study. SSPACE-LongRead is a scaffolder using single molecule long reads to upgrade pre-assembled <t>contigs</t> constructed from short reads. ALLPATHS-LG and SPAdes are hybrid assemblers which take short reads and long reads as inputs. PBcR pipeline uses short reads to correct long reads by pacBioToCA, and then assembles corrected long reads (PBcR) by Celera assembler (runCA). Hierarchical genome-assembly process (HGAP) and PBcR pipeline via self-correction (PBcR pipeline(S)) take long reads as input to produce non-hybrid assembly.
    Contigs, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 1324 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher contigs
    Venn diagram showing distribution of H. glycines BLAST hits by database. Forty-four percent of all 6,860 H. glycines <t>contigs</t> matched sequences in at least one of three databases at a threshold value of 1 e-20 : (a) All cyst nematodes without H. glycines . (b) All non-cyst nematodes. (c) All non-nematodes.
    Contigs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1254 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Roche contigs
    Number of <t>contigs</t> and polymorphisms of various classes and subclasses (y-axis) vs. fold sequence coverage (x-axis). See Table S1.
    Contigs, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 2131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Accelrys contigs
    Number of <t>contigs</t> and polymorphisms of various classes and subclasses (y-axis) vs. fold sequence coverage (x-axis). See Table S1.
    Contigs, supplied by Accelrys, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    CLC Bio contigs
    An overview of the relationships between contig length, population relative abundance and binning accuracy for the TF-ESOM and GroopM approaches. (A) <t>Contigs</t> are ordered from longest to shortest and grouped together into clusters of 50. Each bar represents a single cluster and has a width that is proportional to the total number of assembled bases in that cluster. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned. The large region of unassigned contigs in the TF-ESOM plot reflects the lower binning limit of 2 Kbp for this method. (B) Verified bins are ordered in descending relative abundance, calculated based on the number of simulated reads created using each reference. Each bar represents a single verified bin and the height of each bar represents the bin’s relative abundance. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned by the corresponding method. Both methods had decreased accuracy for very low abundance bins however GroopM was able to correctly bin nearly all the contigs for the most dominant species.
    Contigs, supplied by CLC Bio, used in various techniques. Bioz Stars score: 94/100, based on 1564 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Solexa contigs
    Integrated pipeline for de novo assembly of novel genome sequencing. The scheme is filtering data to remove low-quality and shot-read initial assemblies using variable software and compare to <t>contigs,</t> hybrid contigs using MIRA assembler, and contig ordering using SSPACE software to scaffold construction.
    Contigs, supplied by Solexa, used in various techniques. Bioz Stars score: 92/100, based on 79 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Pacific Biosciences 204 contigs
    Integrated pipeline for de novo assembly of novel genome sequencing. The scheme is filtering data to remove low-quality and shot-read initial assemblies using variable software and compare to <t>contigs,</t> hybrid contigs using MIRA assembler, and contig ordering using SSPACE software to scaffold construction.
    204 Contigs, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc contig assembly
    Integrated pipeline for de novo assembly of novel genome sequencing. The scheme is filtering data to remove low-quality and shot-read initial assemblies using variable software and compare to <t>contigs,</t> hybrid contigs using MIRA assembler, and contig ordering using SSPACE software to scaffold construction.
    Contig Assembly, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 83 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc divergent contigs
    Ranked distribution of the mean interspecific differentiation index ( D − ) between G. firmus and G. pennsylvanicus for each of the 1157 <t>contigs</t> that showed high coverage (≥20×) and at least three SNPs (see Materials and Methods ).
    Divergent Contigs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher mira contigs
    Ranked distribution of the mean interspecific differentiation index ( D − ) between G. firmus and G. pennsylvanicus for each of the 1157 <t>contigs</t> that showed high coverage (≥20×) and at least three SNPs (see Materials and Methods ).
    Mira Contigs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc scaffold contigs
    Ranked distribution of the mean interspecific differentiation index ( D − ) between G. firmus and G. pennsylvanicus for each of the 1157 <t>contigs</t> that showed high coverage (≥20×) and at least three SNPs (see Materials and Methods ).
    Scaffold Contigs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Sources of linking information between contigs. ( A ) overlaps, ( B ) clone mates, ( C ) alignments to reference genome, ( D ) alignments to physical maps, ( E ) conservation of gene synteny.

    Journal: Genome Research

    Article Title: Hierarchical Scaffolding With Bambus

    doi: 10.1101/gr.1536204

    Figure Lengend Snippet: Sources of linking information between contigs. ( A ) overlaps, ( B ) clone mates, ( C ) alignments to reference genome, ( D ) alignments to physical maps, ( E ) conservation of gene synteny.

    Article Snippet: Bambus is required to place all contigs in scaffolds and will thus generally create more scaffolds than Celera Assembler.

    Techniques:

    Detailed information produced by Bambus. Shown are two contigs connected by two valid links (v:2 in the header line), with 1 additional link whose length is outside the estimated range and therefore invalid (l:1). The contigs face away from each other, indicated by the arrows (“→”) in the header. Each pair of linked reads is shown on a separate line, with coordinates indicating the position of the read within its contig. For example, GBRDE74TR is mapped to positions 890-1416 of contig_32, and GBRDE74TF is mapped to positions 413-1207 of contig_38.

    Journal: Genome Research

    Article Title: Hierarchical Scaffolding With Bambus

    doi: 10.1101/gr.1536204

    Figure Lengend Snippet: Detailed information produced by Bambus. Shown are two contigs connected by two valid links (v:2 in the header line), with 1 additional link whose length is outside the estimated range and therefore invalid (l:1). The contigs face away from each other, indicated by the arrows (“→”) in the header. Each pair of linked reads is shown on a separate line, with coordinates indicating the position of the read within its contig. For example, GBRDE74TR is mapped to positions 890-1416 of contig_32, and GBRDE74TF is mapped to positions 413-1207 of contig_38.

    Article Snippet: Bambus is required to place all contigs in scaffolds and will thus generally create more scaffolds than Celera Assembler.

    Techniques: Produced

    Comparison of transcription levels estimation. A . Scaterplot of the number of 454 FLX reads used in the assembly of a given contig versus the number of Illumina reads mapping on the same contig. R1 and R2 stand for the correlation coefficients before and after disregarding the points that exhibit an extreme discrepancy between the two technologies (those ones forming an almost vertical line on the rightmost part of the figure). B . This figure depicts a depth profile showing the reads that map on a given genomic region. The upper part corresponds to 454 FLX, Illumina reads appear in the middle and the last part corresponds to the graphical representation of the corresponding genomic region.

    Journal: BMC Genomics

    Article Title: Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax

    doi: 10.1186/1471-2164-14-149

    Figure Lengend Snippet: Comparison of transcription levels estimation. A . Scaterplot of the number of 454 FLX reads used in the assembly of a given contig versus the number of Illumina reads mapping on the same contig. R1 and R2 stand for the correlation coefficients before and after disregarding the points that exhibit an extreme discrepancy between the two technologies (those ones forming an almost vertical line on the rightmost part of the figure). B . This figure depicts a depth profile showing the reads that map on a given genomic region. The upper part corresponds to 454 FLX, Illumina reads appear in the middle and the last part corresponds to the graphical representation of the corresponding genomic region.

    Article Snippet: Specifically, we compared the number of 454 FLX reads used in the assembly of a given contig versus the number of Illumina reads mapping on the same contig.

    Techniques:

    Schematic overview of our implementation of the MrGBP method to characterise the species relationships among metagenomic contigs.

    Journal: Scientific Reports

    Article Title: A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns

    doi: 10.1038/s41598-018-38197-9

    Figure Lengend Snippet: Schematic overview of our implementation of the MrGBP method to characterise the species relationships among metagenomic contigs.

    Article Snippet: Across-Samples Coverage Information To obtain the coverage profile for contigs across the longitudinal samples, the Illumina reads were mapped to contigs with Bowtie 2 for each time point.

    Techniques:

    Targeted assembly of secondary metabolite synthesizing protein families from the in vitro human oral biofilm MT data set. Only the protein contigs longer than 60aa and nucleotide contigs longer than 180nt were considered. (A) Normalized N50 for protein assembly. (B) Normalized N50 for nucleotide assembly. For (A) and (B), red color indicates the performance of HMMER3 and blue color indicates HMM-GRASPx. The x-axes indicate assembly cases and were sorted based on the decreasing values of the HMMER3 performance and then the decreasing values of the HMM-GRASPx performance. Assembly cases without corresponding red bars indicate that no contig was assembled using HMMER3 predictions. (C) Log2 fold change for the N50 measures in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction. (D) Log2 fold change for the number of assembled reads in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction.

    Journal: PLoS Computational Biology

    Article Title: Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

    doi: 10.1371/journal.pcbi.1004991

    Figure Lengend Snippet: Targeted assembly of secondary metabolite synthesizing protein families from the in vitro human oral biofilm MT data set. Only the protein contigs longer than 60aa and nucleotide contigs longer than 180nt were considered. (A) Normalized N50 for protein assembly. (B) Normalized N50 for nucleotide assembly. For (A) and (B), red color indicates the performance of HMMER3 and blue color indicates HMM-GRASPx. The x-axes indicate assembly cases and were sorted based on the decreasing values of the HMMER3 performance and then the decreasing values of the HMM-GRASPx performance. Assembly cases without corresponding red bars indicate that no contig was assembled using HMMER3 predictions. (C) Log2 fold change for the N50 measures in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction. (D) Log2 fold change for the number of assembled reads in assembly cases where contigs can be assembled using either HMMER3 or HMM-GRASPx prediction.

    Article Snippet: The resulting assembled contigs are available online at https://sourceforge.net/projects/hmm-graspx/files/SupplementaryData/SalivaAssembledContigs.faa.tgz .

    Techniques: In Vitro

    Distributions of ESTs in Contigs . Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.

    Journal: BMC Genomics

    Article Title: Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

    doi: 10.1186/1471-2164-11-606

    Figure Lengend Snippet: Distributions of ESTs in Contigs . Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.

    Article Snippet: The 2258 contigs were manually checked and the longest EST from each contig was selected as unigene.

    Techniques:

    Distribution of BAC hits and contig/marker . (a) the distribution of BAC hits/marker using 1470 markers; (b) the distribution of the numbers of identified contigs of each marker.

    Journal: BMC Genomics

    Article Title: Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    doi: 10.1186/1471-2164-9-28

    Figure Lengend Snippet: Distribution of BAC hits and contig/marker . (a) the distribution of BAC hits/marker using 1470 markers; (b) the distribution of the numbers of identified contigs of each marker.

    Article Snippet: Of these contigs, 458 (35.1%) have only one unigene, 772 (59.1%) contigs have 2~8 unigenes, and 75 (5.7%) contigs have 9~44 unigenes.

    Techniques: BAC Assay, Marker

    Example of the integrated map view of a ~8 cM region on LG E . The genetic map was redrawn based on the integrated genetic linkage map [11]. The QTL name and position refer to the Soybean Breeders Toolbox [34]. The dashed lines indicate the discrepancies of marker alignments between the physical map and genetic map. The highlighted FPC contigs are questionable. The number above the lines connecting genetic markers and contigs is the number of BAC hits. The white bars between highlight bars are gaps between the WSS scaffolds.

    Journal: BMC Genomics

    Article Title: Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    doi: 10.1186/1471-2164-9-28

    Figure Lengend Snippet: Example of the integrated map view of a ~8 cM region on LG E . The genetic map was redrawn based on the integrated genetic linkage map [11]. The QTL name and position refer to the Soybean Breeders Toolbox [34]. The dashed lines indicate the discrepancies of marker alignments between the physical map and genetic map. The highlighted FPC contigs are questionable. The number above the lines connecting genetic markers and contigs is the number of BAC hits. The white bars between highlight bars are gaps between the WSS scaffolds.

    Article Snippet: Of these contigs, 458 (35.1%) have only one unigene, 772 (59.1%) contigs have 2~8 unigenes, and 75 (5.7%) contigs have 9~44 unigenes.

    Techniques: Marker, BAC Assay

    Comparisons of the assemblers conducted in this study. SSPACE-LongRead is a scaffolder using single molecule long reads to upgrade pre-assembled contigs constructed from short reads. ALLPATHS-LG and SPAdes are hybrid assemblers which take short reads and long reads as inputs. PBcR pipeline uses short reads to correct long reads by pacBioToCA, and then assembles corrected long reads (PBcR) by Celera assembler (runCA). Hierarchical genome-assembly process (HGAP) and PBcR pipeline via self-correction (PBcR pipeline(S)) take long reads as input to produce non-hybrid assembly.

    Journal: Scientific Reports

    Article Title: Completing bacterial genome assemblies: strategy and performance comparisons

    doi: 10.1038/srep08747

    Figure Lengend Snippet: Comparisons of the assemblers conducted in this study. SSPACE-LongRead is a scaffolder using single molecule long reads to upgrade pre-assembled contigs constructed from short reads. ALLPATHS-LG and SPAdes are hybrid assemblers which take short reads and long reads as inputs. PBcR pipeline uses short reads to correct long reads by pacBioToCA, and then assembles corrected long reads (PBcR) by Celera assembler (runCA). Hierarchical genome-assembly process (HGAP) and PBcR pipeline via self-correction (PBcR pipeline(S)) take long reads as input to produce non-hybrid assembly.

    Article Snippet: Dozens of contigs were generated even if the PacBio long reads were used, and the N50 values obtained from SPAdes were as low as one tenth of the values obtained from ALLPATHS-LG.

    Techniques: Construct

    Venn diagram showing distribution of H. glycines BLAST hits by database. Forty-four percent of all 6,860 H. glycines contigs matched sequences in at least one of three databases at a threshold value of 1 e-20 : (a) All cyst nematodes without H. glycines . (b) All non-cyst nematodes. (c) All non-nematodes.

    Journal: Genome Biology

    Article Title: Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

    doi: 10.1186/gb-2007-8-10-r211

    Figure Lengend Snippet: Venn diagram showing distribution of H. glycines BLAST hits by database. Forty-four percent of all 6,860 H. glycines contigs matched sequences in at least one of three databases at a threshold value of 1 e-20 : (a) All cyst nematodes without H. glycines . (b) All non-cyst nematodes. (c) All non-nematodes.

    Article Snippet: Contigs were formed by Affymetrix for the design of the H. glycines group of probesets of the Affymetrix Soybean Genome Array GeneChip and all consensus sequences and contig size details can be accessed at Affymetrix [ ].

    Techniques:

    A schematic overview of CISA. Phase (1): employing the largest contig as a representative contig and identifying the contigs which were aligned to the ends of the representative contig with more than 80% alignment to perform possible extension (hollow ellipses and solid arrows represent before and after extension, respectively). Phase (2): removing and splitting misassembled contigs. Two misassembled contigs are shown in black. The left element represents a misjoined error because it was assembled in two different contigs in two individual assemblies (blue and red); the right element represents an insertion error (dot), which was never seen in other assemblies. Phase (3): iteratively merging contigs with a proper end-to-end overlap and estimating the size of repetitive regions. Phase (4): merging two contigs with a small overlap greater than the maximum size of repetitive regions.

    Journal: PLoS ONE

    Article Title: CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

    doi: 10.1371/journal.pone.0060843

    Figure Lengend Snippet: A schematic overview of CISA. Phase (1): employing the largest contig as a representative contig and identifying the contigs which were aligned to the ends of the representative contig with more than 80% alignment to perform possible extension (hollow ellipses and solid arrows represent before and after extension, respectively). Phase (2): removing and splitting misassembled contigs. Two misassembled contigs are shown in black. The left element represents a misjoined error because it was assembled in two different contigs in two individual assemblies (blue and red); the right element represents an insertion error (dot), which was never seen in other assemblies. Phase (3): iteratively merging contigs with a proper end-to-end overlap and estimating the size of repetitive regions. Phase (4): merging two contigs with a small overlap greater than the maximum size of repetitive regions.

    Article Snippet: Since a contig may bridge two contigs, the merge processes were performed iteratively until there was no sequence alignment with over 30% alignment rate.

    Techniques:

    Integration of five assemblies of 36 bp paired-end reads for E. coli using CISA and minimus2. (A) From left to right, CISA integrates the five assemblies (Abyss, CLC, Edena, SOAPdenovo and Velvet from the outer to the inner) and sequentially generates the processed contigs after phase (1), (2), (3), and (4). Each contig color is randomly assigned. The white and grey segments in the inner circle show missing and laying of contigs in the genome. The dark-grey segments represent overlaps between contigs. (B) From left to right, minimus2 firstly merges SOAPdenovo (the inner) with CLC (the outer), then merges the output (the inner) with Velvet (the outer) in the second run, merges the output (the inner) with Edena (the outer) in the third run, and finally merges the output (the inner) with Abyss (the outer) in the fourth run to generate a hybrid assembly.

    Journal: PLoS ONE

    Article Title: CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

    doi: 10.1371/journal.pone.0060843

    Figure Lengend Snippet: Integration of five assemblies of 36 bp paired-end reads for E. coli using CISA and minimus2. (A) From left to right, CISA integrates the five assemblies (Abyss, CLC, Edena, SOAPdenovo and Velvet from the outer to the inner) and sequentially generates the processed contigs after phase (1), (2), (3), and (4). Each contig color is randomly assigned. The white and grey segments in the inner circle show missing and laying of contigs in the genome. The dark-grey segments represent overlaps between contigs. (B) From left to right, minimus2 firstly merges SOAPdenovo (the inner) with CLC (the outer), then merges the output (the inner) with Velvet (the outer) in the second run, merges the output (the inner) with Edena (the outer) in the third run, and finally merges the output (the inner) with Abyss (the outer) in the fourth run to generate a hybrid assembly.

    Article Snippet: Since a contig may bridge two contigs, the merge processes were performed iteratively until there was no sequence alignment with over 30% alignment rate.

    Techniques:

    Number of contigs and polymorphisms of various classes and subclasses (y-axis) vs. fold sequence coverage (x-axis). See Table S1.

    Journal: PLoS ONE

    Article Title: Using Genomic Sequencing for Classical Genetics in E. coli K12

    doi: 10.1371/journal.pone.0016717

    Figure Lengend Snippet: Number of contigs and polymorphisms of various classes and subclasses (y-axis) vs. fold sequence coverage (x-axis). See Table S1.

    Article Snippet: Our data and parameters were: CDS sequences of the reference genome, MG1655 (NC_000913); genomic sequence of contigs assembled de novo by Roche using Newbler; blastn with default parameters; e-value cutoff 0.0001; DAGChainer options −g 5 −D 20 −A 5.

    Techniques: Sequencing

    Syntenic dotplots of de novo assembled contigs of NCM4370 (x-axis) to fully sequenced and assembled reference genome MG1655. Vertical black lines separate contigs from NCM4370. Gray dots are putative homologous gene pairs. Green dots (which form lines) are collinear sets of homologous gene pairs used to infer synteny. (A) NCM4370 contigs are ordered by size with largest on the left ( http://genomevolution.org/r/bjz ). The largest contigs are in the region of the terminus of replication, which is known to contain fewer repetitive elements than other regions of the E. coli genome [46] . (B) NCM4370 contigs are ordered in the best syntenic path by comparison to reference genome MG1655. Individual contigs may be inverted to ensure that the syntenic path is conserved. Discontinuities in syntenic line are the result of deletions and insertions. The red arrow marks the position of a lambda prophage in NCM4370 (see text). Results can be regenerated at: http://genomevolution.org/r/bjy .

    Journal: PLoS ONE

    Article Title: Using Genomic Sequencing for Classical Genetics in E. coli K12

    doi: 10.1371/journal.pone.0016717

    Figure Lengend Snippet: Syntenic dotplots of de novo assembled contigs of NCM4370 (x-axis) to fully sequenced and assembled reference genome MG1655. Vertical black lines separate contigs from NCM4370. Gray dots are putative homologous gene pairs. Green dots (which form lines) are collinear sets of homologous gene pairs used to infer synteny. (A) NCM4370 contigs are ordered by size with largest on the left ( http://genomevolution.org/r/bjz ). The largest contigs are in the region of the terminus of replication, which is known to contain fewer repetitive elements than other regions of the E. coli genome [46] . (B) NCM4370 contigs are ordered in the best syntenic path by comparison to reference genome MG1655. Individual contigs may be inverted to ensure that the syntenic path is conserved. Discontinuities in syntenic line are the result of deletions and insertions. The red arrow marks the position of a lambda prophage in NCM4370 (see text). Results can be regenerated at: http://genomevolution.org/r/bjy .

    Article Snippet: Our data and parameters were: CDS sequences of the reference genome, MG1655 (NC_000913); genomic sequence of contigs assembled de novo by Roche using Newbler; blastn with default parameters; e-value cutoff 0.0001; DAGChainer options −g 5 −D 20 −A 5.

    Techniques:

    A series of syntenic dotplots between the NCM strains and the reference genome MG1655. Scaffolds of the NCM strains are ordered by their syntenic path to MG1655. Vertical black lines are divisions between contigs and green diagonal lines are syntenic gene pairs. Red arrows show an additional contig break in NCM4139 and NCM4384 caused by a new insertion of IS186 in the promoter for the lon gene. The extra breaks in strain NCM4781, which were due to insufficient sequence coverage, are immediately apparent.

    Journal: PLoS ONE

    Article Title: Using Genomic Sequencing for Classical Genetics in E. coli K12

    doi: 10.1371/journal.pone.0016717

    Figure Lengend Snippet: A series of syntenic dotplots between the NCM strains and the reference genome MG1655. Scaffolds of the NCM strains are ordered by their syntenic path to MG1655. Vertical black lines are divisions between contigs and green diagonal lines are syntenic gene pairs. Red arrows show an additional contig break in NCM4139 and NCM4384 caused by a new insertion of IS186 in the promoter for the lon gene. The extra breaks in strain NCM4781, which were due to insufficient sequence coverage, are immediately apparent.

    Article Snippet: Our data and parameters were: CDS sequences of the reference genome, MG1655 (NC_000913); genomic sequence of contigs assembled de novo by Roche using Newbler; blastn with default parameters; e-value cutoff 0.0001; DAGChainer options −g 5 −D 20 −A 5.

    Techniques: Sequencing

    An overview of the relationships between contig length, population relative abundance and binning accuracy for the TF-ESOM and GroopM approaches. (A) Contigs are ordered from longest to shortest and grouped together into clusters of 50. Each bar represents a single cluster and has a width that is proportional to the total number of assembled bases in that cluster. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned. The large region of unassigned contigs in the TF-ESOM plot reflects the lower binning limit of 2 Kbp for this method. (B) Verified bins are ordered in descending relative abundance, calculated based on the number of simulated reads created using each reference. Each bar represents a single verified bin and the height of each bar represents the bin’s relative abundance. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned by the corresponding method. Both methods had decreased accuracy for very low abundance bins however GroopM was able to correctly bin nearly all the contigs for the most dominant species.

    Journal: PeerJ

    Article Title: GroopM: an automated tool for the recovery of population genomes from related metagenomes

    doi: 10.7717/peerj.603

    Figure Lengend Snippet: An overview of the relationships between contig length, population relative abundance and binning accuracy for the TF-ESOM and GroopM approaches. (A) Contigs are ordered from longest to shortest and grouped together into clusters of 50. Each bar represents a single cluster and has a width that is proportional to the total number of assembled bases in that cluster. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned. The large region of unassigned contigs in the TF-ESOM plot reflects the lower binning limit of 2 Kbp for this method. (B) Verified bins are ordered in descending relative abundance, calculated based on the number of simulated reads created using each reference. Each bar represents a single verified bin and the height of each bar represents the bin’s relative abundance. Bars are split vertically according to the percentage of their bases that are either correctly, incorrectly or not assigned by the corresponding method. Both methods had decreased accuracy for very low abundance bins however GroopM was able to correctly bin nearly all the contigs for the most dominant species.

    Article Snippet: Of the contigs that Velvet did produce, the binning was consistent with the CLC Bio and SPAdes-derived bins.

    Techniques:

    A comparison of GroopM and Sharon bin assignments generated using visualization tools within GroopM. (A) Contigs and resulting bins made using SPAdes and GroopM. (B) The Sharon assembly visualized in GroopM coverage space. All the contigs belonging to a single bin are assigned the same color. Each bin was assigned a random unique color with the exception of strain variants which were assigned very similar colors. GroopM-binned contigs are colored according to the bin assignment of their closest matching contig in the Sharon assembly.

    Journal: PeerJ

    Article Title: GroopM: an automated tool for the recovery of population genomes from related metagenomes

    doi: 10.7717/peerj.603

    Figure Lengend Snippet: A comparison of GroopM and Sharon bin assignments generated using visualization tools within GroopM. (A) Contigs and resulting bins made using SPAdes and GroopM. (B) The Sharon assembly visualized in GroopM coverage space. All the contigs belonging to a single bin are assigned the same color. Each bin was assigned a random unique color with the exception of strain variants which were assigned very similar colors. GroopM-binned contigs are colored according to the bin assignment of their closest matching contig in the Sharon assembly.

    Article Snippet: Of the contigs that Velvet did produce, the binning was consistent with the CLC Bio and SPAdes-derived bins.

    Techniques: Generated

    The distribution of tetranucleotide frequencies, coverage profiles and bin assignments for the synthetic metagenomic contigs. The diameter of each circle is proportional to the length its respective contig. (A, C, E) Contigs are positioned according to the first two principal components of their tetranucleotide frequencies. The first principal component is positioned horizontally, the second is positioned vertically. (B, D, F) Contigs are positioned according to their x and y coordinates in GroopM transformed coverage profile space. (A, B) Each ‘true’ bin is assigned a random color and contigs are colored according to their true bin assignments. (C, D) Contigs are colored according to the accuracy of their bin assignments using TF-ESOM. (E, F) Contigs are colored according to the accuracy of their bin assignments using GroopM.

    Journal: PeerJ

    Article Title: GroopM: an automated tool for the recovery of population genomes from related metagenomes

    doi: 10.7717/peerj.603

    Figure Lengend Snippet: The distribution of tetranucleotide frequencies, coverage profiles and bin assignments for the synthetic metagenomic contigs. The diameter of each circle is proportional to the length its respective contig. (A, C, E) Contigs are positioned according to the first two principal components of their tetranucleotide frequencies. The first principal component is positioned horizontally, the second is positioned vertically. (B, D, F) Contigs are positioned according to their x and y coordinates in GroopM transformed coverage profile space. (A, B) Each ‘true’ bin is assigned a random color and contigs are colored according to their true bin assignments. (C, D) Contigs are colored according to the accuracy of their bin assignments using TF-ESOM. (E, F) Contigs are colored according to the accuracy of their bin assignments using GroopM.

    Article Snippet: Of the contigs that Velvet did produce, the binning was consistent with the CLC Bio and SPAdes-derived bins.

    Techniques: Transformation Assay

    Integrated pipeline for de novo assembly of novel genome sequencing. The scheme is filtering data to remove low-quality and shot-read initial assemblies using variable software and compare to contigs, hybrid contigs using MIRA assembler, and contig ordering using SSPACE software to scaffold construction.

    Journal: Genomics & Informatics

    Article Title: Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling

    doi: 10.5808/GI.2012.10.1.1

    Figure Lengend Snippet: Integrated pipeline for de novo assembly of novel genome sequencing. The scheme is filtering data to remove low-quality and shot-read initial assemblies using variable software and compare to contigs, hybrid contigs using MIRA assembler, and contig ordering using SSPACE software to scaffold construction.

    Article Snippet: Even though numerous contigs assembled with Illumina/Solexa data were produced in the eukaryotic genome, a few drafts for the assembled genome sequence were reported, except for the giant panda genome [ ], which was covered with assembled contigs (2.25 Gb), covering approximately 94% of the expected whole genome.

    Techniques: Sequencing, Software

    Ranked distribution of the mean interspecific differentiation index ( D − ) between G. firmus and G. pennsylvanicus for each of the 1157 contigs that showed high coverage (≥20×) and at least three SNPs (see Materials and Methods ).

    Journal: Genetics

    Article Title: Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

    doi: 10.1534/genetics.112.142299

    Figure Lengend Snippet: Ranked distribution of the mean interspecific differentiation index ( D − ) between G. firmus and G. pennsylvanicus for each of the 1157 contigs that showed high coverage (≥20×) and at least three SNPs (see Materials and Methods ).

    Article Snippet: Using Sanger sequencing in a larger sample of crickets from the same allopatric populations, we confirmed that a sample of divergent contigs identified from Illumina reads indeed represents sequences that are highly divergent between the two cricket populations.

    Techniques:

    DNA gene genealogies for a subset of 10 highly differentiated contigs and two seminal fluid protein genes ( AG-0005F and AG-0334P ). G. firmus is represented by open circles and G. pennsylvanicus by solid circles. Size of symbols is proportional to the

    Journal: Genetics

    Article Title: Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

    doi: 10.1534/genetics.112.142299

    Figure Lengend Snippet: DNA gene genealogies for a subset of 10 highly differentiated contigs and two seminal fluid protein genes ( AG-0005F and AG-0334P ). G. firmus is represented by open circles and G. pennsylvanicus by solid circles. Size of symbols is proportional to the

    Article Snippet: Using Sanger sequencing in a larger sample of crickets from the same allopatric populations, we confirmed that a sample of divergent contigs identified from Illumina reads indeed represents sequences that are highly divergent between the two cricket populations.

    Techniques: