celera/arachne contigs  (Celera)

Journal: PLoS ONE

Article Title: GRASShopPER—An algorithm for de novo assembly based on GPU alignments

doi: 10.1371/journal.pone.0202355

Figure Lengend Snippet: The method has three main steps: construction of the overlap graph, its traversal, and correction of contigs.

Article Snippet: Even bigger disappointment comes from the Celera contigs genome fraction, which together with its outlying result on the largest alignment and NG50 makes Celera inferior on this data set.

Techniques:

Journal: PLoS ONE

Article Title: GRASShopPER—An algorithm for de novo assembly based on GPU alignments

doi: 10.1371/journal.pone.0202355

Figure Lengend Snippet: Assemblies obtained for three data sets: C . Microthrix, C. elegans , and human chromosome 14 (metrics calculated by QUAST).

Article Snippet: Even bigger disappointment comes from the Celera contigs genome fraction, which together with its outlying result on the largest alignment and NG50 makes Celera inferior on this data set.

Techniques:

Journal: Nature methods

Article Title: Assembly and diploid architecture of an individual human genome via single-molecule technologies

doi: 10.1038/nmeth.3454

Figure Lengend Snippet: De novo assembly and scaffold layout. PacBio sequence contigs. Genome maps and scaffold V2 are shown in order from the top of each chromosome, with the hg19 reference at the bottom. Possible chimeras identified by comparison of sequence contigs and genome maps (but not those that persist in the V2 scaffold) are indicated in cyan (flagged assembly). Ideogram and Giemsa banding for hg19 is plotted at the bottom of each chromosome in grayscale, with centromeres highlighted in light red. ‘N’ gaps in hg19 are shaded with gray in the background of all assemblies and scaffolds.

Article Snippet: Finally, to anchor the original sequences and generate FASTA sequences, we realigned the sequence maps with the V2 hybrid scaffolds using custom scripts ( Supplementary Note 3 ), and any V2 scaffolds formed solely from Falcon overlaps (5) that did not have Celera-assembled contigs mapping support were eliminated (3).

Techniques: Sequencing

Journal: Nature methods

Article Title: Assembly and diploid architecture of an individual human genome via single-molecule technologies

doi: 10.1038/nmeth.3454

Figure Lengend Snippet: Assembly and scaffold summary statistics

Article Snippet: Finally, to anchor the original sequences and generate FASTA sequences, we realigned the sequence maps with the V2 hybrid scaffolds using custom scripts ( Supplementary Note 3 ), and any V2 scaffolds formed solely from Falcon overlaps (5) that did not have Celera-assembled contigs mapping support were eliminated (3).

Techniques: Sequencing

Journal: Scientific Reports

Article Title: Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

doi: 10.1038/srep10814

Figure Lengend Snippet: Evaluation of the performance of de novo genome assembly using MIRA and Celera.

Article Snippet: To evaluate the characteristics of the contigs assembled with Celera (8.1) or MIRA (4.0.1), the prevalence of SNVs, indels and other mis-assembly events were calculated using the QUAST (2.3) .

Techniques:

Journal: Scientific Reports

Article Title: Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

doi: 10.1038/srep10814

Figure Lengend Snippet: ( A ) Plotting of contig N50 length against the sequencing depth. ( B , C and D ) Plotting of read (blue) and contig (red and green) coverage of genome, protein-coding genes and repetitive sequences against the sequencing depth respectively. Contigs were assembled using Celera (red) or MIRA (green) assembler with 3×, 6×, 12× and 24× reads.

Article Snippet: To evaluate the characteristics of the contigs assembled with Celera (8.1) or MIRA (4.0.1), the prevalence of SNVs, indels and other mis-assembly events were calculated using the QUAST (2.3) .

Techniques: Sequencing