Results for "Pacbio"
Blogs
Software and Tools to detect structure variation with long reads !!
...es and types in a genome. While a PacBio de novo assembly re...the most novel SV variants. 8-10X PacBio coverage of single genomes or...sing third generation sequencing (PacBio or Oxford Nanopore). It detec...ural variant and indel caller for PacBio reads Structural variant (SV...2592 days ago
BBTools for bioinformatician !
...ieces and mapped independently. Code: $ mapPacBio.sh -Xmx20g k=7 in=reads.fastq...e generated on the basis of quality; there's a PacBio error model; and all of the r...e generated on the basis of quality; there's a PacBio error model; and all of the r...2255 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...3588 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...d also presents a significant improvement over the state-of-the-art for PacBio read mappers. GraphMap was a...ange of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore...3209 days ago
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Files
- .... With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this...
808 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...uence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only...em under the minimum-error-correction (MEC) model. PBSIM 1.0.3 – PacBio Reads SimulatorPacBio sequenc...2670 days ago
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...s 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 fl...2670 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...lding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes) Softwa...Mash Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHa...2355 days ago
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Wire posts
News
Phased Human Genome Assembly !
...new publicly available assembly (PacBio HG00733) has the fewest...contigs that were assembled with PacBio data generated with the compa...the assembly are included on the PacBio blog. The data are available...More details are available on the PacBio website: Blog post: D...2020 days ago
Video
Genome + Epigenome = New Understanding of the Pathogens in Your Food
...Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close...3857 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
2236 days ago
Long reads mapper bash script !
...== "ont" ]; then $lamsaLoc aln -t $thread -T ont2d $refFasta $longReads > $fileName.out.sam elif [ $readsType == "pacbio" ]; then $lamsaLoc aln -t $thread -T pacbio $refFasta $longReads > $fileN...2107 days ago
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Groups
Single molecule Sequencing (SMS)
...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 the...3211 days ago
Tags
Software and Tools to detect structure variation with long reads !!
Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs ...Tags: Bioinformatics, LR, Long, Reads, Tools, Software, Pacbio, Genome, DNA, Sequence, NGS, SV, Variation, Structure
2592 days ago
Understating pacbio reads name !
m140415_143853_42175_c100635972550000001823121909121417_s1_p0/553/3100_11230 0.99 24 └1┘└─────2─────┘└──3─┘└────────────────4────────────────┘└5┘└6┘└7┘└────8────┘└─9─┘└10┘ "m" = movie Time of Run Start (yymmdd_hhmmss) Instrument Serial Number SMRT Cell Barcode Set Number (a.k.a. "L...Tags: pacbio, file, name, explanation
1974 days ago
Comments
- ...different sequencing technologies, including Illumina, Ion Torrent, and PacBio. PIRS allows users to customi...simulate reads from different sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. It can...
400 days ago
Comment on "Short-read assembly using Spades !"
...SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, IonTorrent, PacBio, and Oxford Nanopore sequenci...405 days ago
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