Results for "pacbio smrt"
Blogs
Software and Tools to detect structure variation with long reads !!
...p;Single Molecule, Real-Time (SMRT) Sequencing, you can access str...third generation sequencing (PacBio or Oxford Nanopore). It detec...forge.net/projects/pb-jelly/ SMRT-SV: Structural variant and indel caller for PacBio reads Structural variant (...2622 days ago
BBTools for bioinformatician !
BBMap.sh Mapping Nanopore reads BBMap.sh has a length cap of 6kbp. R...mapped independently. Code: $ mapPacBio.sh -Xmx20g k=7 in=reads.fastq...ed on the basis of quality; there's a PacBio error model; and all of the r...ed on the basis of quality; there's a PacB...2285 days ago
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Bookmarks
Bioinformatics algorithms tutorials
Useful bioinformatics tutorial, such as De Bruijn Graphs for NGS AssemblyAlgorithms for PacBio ReadsSoftware and Hardware Concepts for BioinformaticsFinding us in Homolog.us (Search Algorithms)NG...3617 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap is a novel mapper targeted at aligning long, error-prone third-generation seque...gnificant improvement over the state-of-the-art for PacBio read mappers. GraphMap was a...and error profiles, including: Illumina, PacB...3239 days ago
- +59 more Bookmarks
Files
- SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencin...embly of IonTorrent data, as well as hybrid assembly from short and long reads (PacB...
838 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
The genome assemblers generally take a file of short sequence reads and a file of qualit...Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only...-error-correction (MEC) model. PBSIM 1.0.3 – PacB...2700 days ago
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...from Long Gapless Reads A fast and memory-efficient method for haplotype assembly from long gapless reads, like those produced by SMRT sequencing technologies (PacBio RS II) and Oxford Nanopore...2700 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
.../MHAP Miniasm Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout...h error-containing long sequence (e.g., ONT or PacBio reads, draft genomes) Softwa...ation using assembled or unassembled Illumina, PacBio, and ONT data (based on Min...2385 days ago
- +5 more Top-level pages
Wire posts
News
Phased Human Genome Assembly !
...publicly available assembly (PacBio HG00733) has the fewest...tigs that were assembled with PacBio data generated with the compa...assembly are included on the PacBio blog. The data are available...details are available on the PacBio website: Blog post: D...2050 days ago
Video
Genome + Epigenome = New Understanding of the Pathogens in Your Food
UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacB...3887 days ago
Bio-Scripts
- # generate dotplot lastdb test/ref.fa lastal -f TAB test/ref.fa test/contigs.reduced.pacbio.fa | last-dotplot - test/contigs.reduced.pacbio.fa.ref.png lastal -f TAB test/ref.fa test/contigs.reduced.nanopore.fa | last-dotplot - test/contigs.reduced.nanopore.fa.ref.png
2266 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont...d $refFasta $longReads > $fileName.out.sam elif [ $readsType == "pacbio" ]; then $lamsaLoc aln -t $thread -T pacb...2137 days ago
- +5 more Bio-Scripts
Groups
Single molecule Sequencing (SMS)
...ntists now keen to use SMS method to sequence molecules in comparatively less complex protocal and less time. One of most successful so far is SMRT from Pacbio and others will be flood th...3241 days ago
Comments
Comment on "LAMSA: fast split read alignment with long approximate matches"
...hin reads. [0.04] -T --read-type [STR] Specifiy the type of reads and set multiple parameters unless overriden. [null] (Illumina Moleculo) pacbio (PacBio SMRT): -i25 -l50 -m1 -M1 -O1,1,2,2...2137 days ago
