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All (23)
Illumina
Oxford Nanopore
Pacific Biosciences
SourceForge net
BioNano
Broad Institute
MYCO Medical
Sentieon
15 More...
 

About 50 products / 203 snippets / 27 images

91 / 100
Bioz Stars
Minimap2
Illumina  
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Techniques
 
Article Snippets
"Minimap2 ( ) and Kraken 2.0.8-beta ( ) were used to identify the best matching species for each 10x Chromium genomic DNA read (from Illumina HiSeq X and HiSeq4000 platforms)."  (see more)
80 / 100
Bioz Stars
Minimap2
Oxford Nanopore  
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Techniques
 
Article Snippets
"Then, Illumina short reads were corrected using prepared Oxford Nanopore reads by minimap2 (v. 2.24-r1122) (ten cycles) [ ] and racon (v. 1.4.13) [ ]."  (see more)
23+  more images
Characterization of aligned reads. A. Total number of reads and the number of reads with a primary alignment to the genome or transcriptome, respectively, in each of the ONT libraries. The number displayed in each bar represents the alignment rate in % (the fraction of the total number of reads for which <t>minimap2</t> reports a primary alignment). B. Fraction of the reads with a primary alignment to the genome or transcriptome, respectively, that also have at least one reported secondary or supplementary alignment. The lighter shaded parts of the secondary transcriptome alignment bars correspond to reads where all primary and secondary alignments are to isoforms of the same gene, while the darker shaded parts correspond to reads with reported alignments to transcripts from different genes. C. Investigation of supplementary genome alignments. Each supplementary alignment is categorized based on whether it is on the same chromosome and strand as the primary alignment, and if the alignment positions of the primary and supplementary alignments overlap.
( A ) and locus- or block-level ( B ) alignment accuracy from synthetic long reads. The x-axis shows the error rate alignments (see Materials and Methods). The y-axis shows the fraction of aligned reads out of all input reads. Each point in the plot corresponds to a mapping quality threshold that varies from 0 (top right) to 60 (bottom left). ( C ) and ( D ): Alignment statistics for real Nanopore whole genome sequencing data from using a 16-part index. ( C ) The number of total entries (primary+secondary+unaligned) for single-idx , 16-part-idx-merged , and 16-part-idx-no-merge , in log scale. The dotted horizontal line represents the number of reads. (D) Number of primary mappings in function of <t>Minimap2</t> mapping quality (log scale).
BLOCK-A
SEQ
RECOMB
EXT
BCA-P
BLOCK-A
LYSIS
Following the acquisition of raw sequence data produced by MinKNOW during a nanopore run, Guppy is used to rebasecall data, trim the adapter sequence, reverse the orientation of the sequence read (from 3’->5’ to 5’->3’), and replace uracil bases with thymine bases. Processed sequence reads are aligned against a chosen reference genome sequence using <t>MiniMap2</t> and (optionally) Illumina data are used in conjunction with FLAIR to perform splice-site correction. At this stage, aligned datasets may be visualized using standard tools such as IGV or GVIZ before subsequent processing to produce transcript abundance counts (using custom scripts) and/or to identify TSS and CPAS (using Homer).
SEQ
PROD
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88 / 100
Bioz Stars
Minimap2
NanoPack  
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Techniques
 
Article Snippets
".. NanoFilt, a component from Nanopack [ ], with settings ‘-q 0 --headcrop 5 --tailcrop 3’, and mapped to the 4 synthetic sequences using minimap2 [ ] with the settings -ax .."  (see more)
80 / 100
Bioz Stars
Minimap2
Pacific Biosciences  
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Techniques
 
Article Snippets
"First, the raw CLR PacBio reads were mapped using the PacBio version of minimap2 ( https://github.com/PacificBiosciences/pbmm2 ) and then polished using variantCaller v.2.3.3."  (see more)
80 / 100
Bioz Stars
Minimap2 minimap2-fpga
Xilinx  
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Techniques
 
Article Snippets
".. Fr ac o n of m ap pe d re ad s minimap2 minimap2-fpga (Intel FPGA-based) minimap2-fpga (Xilinx FPGA-based) 10 -6 10 -5 10 -4 10 -3 10 -2 Error .."  (see more)
92 / 100
Bioz Stars
In Minimap2
Oxford Nanopore  
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Techniques
 
Article Snippets
"In fact, the default k-mer size for Oxford Nanopore in Minimap2 (set by map-ont pre-set) is 15."  (see more)
BLOCK-A
SEQ
91 / 100
Bioz Stars
Minimap2
Sentieon  
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Techniques
 
Article Snippets
"In the pre-processing stage, Sentieon Minimap2 (Li, 2018), an accelerated version of the opensource Minimap2, is used to map reads to either amplicon sequences or reference genome."  (see more)
80 / 100
Bioz Stars
Minimap2
Biocrates  
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Techniques
 
Article Snippets
"The reads were mapped using minimap2 (biocrates life sciences, Innsbruck, Austria) to the human reference genome (GRCh38) that contains 27 repeats in ACAN VNTR."  (see more)
80 / 100
Bioz Stars
Minimap2
The Jackson Laboratory  
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Techniques
 
Article Snippets
".. alignments from different aligners including NGMLR and minimap2 ( https://github.com/TheJacksonLaboratory/Picky/wiki/Using-an-Alternative-Aligner )."  (see more)
90 / 100
Bioz Stars
Minimap2
BioNano  
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Techniques
 
Article Snippets
".. and orientation of fluorescently-labeled sequence motifs Example algorithms/programs BreakDancer; LUMPY; Manta SMRT-SV (PacBio); Minimap2; MuMmer; Bionano SVCaller NanoVar (ONT) Graphtyper2 Proportion of SVs discovered across the genome Moderate High .."  (see more)
80 / 100
Bioz Stars
Minimap2
Bambu Vault  
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Techniques
 
Article Snippets
".. for later demultiplexing; second, the labelled reads are aligned to the genome with Minimap2 ; third, Bambu-Clump is executed for read class construction, transcript discovery, and single cell quantification. .."  (see more)
CONST
RNAseq
SEQ
80 / 100
Bioz Stars
Minimap2
Broad Institute  
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Techniques
 
Article Snippets
".. files were collected and mapped against a SARS-CoV-2 reference genome (Wuhan-Hu-1/2020; NC_045512) by minimap2 (v2.17; Broad Institute of MIT and Harvard, Cambridge, MA, USA) -x sr for Illumina NovaSeq, map-ont .."  (see more)