Results for "PacBio RSII"
Blogs
Software and Tools to detect structure variation with long reads !!
Uncovering the connection between genetics and heritable diseases...nd types in a genome. While a PacBio de novo assembly re...most novel SV variants. 8-10X PacBio coverage of single genomes or...third generation sequencing (PacBio or Oxford Nanopore). It detec...variant and indel caller for PacB...2654 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...2317 days ago
- +5 more Blogs
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...3649 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...3271 days ago
- +55 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...
870 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...2732 days ago
Top-level pages
Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since...y from long gapless reads, like those produced by SMRT sequencing technologies (PacB...2732 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignm...y with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes) Softwa...tification using assembled or unassembled Illumina, PacB...2417 days ago
- +5 more Top-level pages
Wire posts
News
Phased Human Genome Assembly !
The new publicly available assembly (PacBio HG00733) has the fewest gaps of...865 contigs that were assembled with PacBio data generated with the compa...out the assembly are included on the PacBio blog. The data are available...More details are available on the PacB...2082 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...3919 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
2298 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...2169 days ago
- +5 more Bio-Scripts
Groups
Single molecule Sequencing (SMS)
SMS is now slowly gaining place in sequencing world, more and more scientists now keen to use SMS method to sequence...less complex protocal and less time. One of most successful so far is SMRT from Pacb...3273 days ago
Comments
Comment on "Want to Know which genome assembler rule the world ?"
Canu Assembler is my personal favourate.Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequelor Oxford Nanopore MinION).1996 days ago
