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...2746 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...2409 days ago
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...3742 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...3363 days ago
963 days ago
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...2824 days ago
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...2824 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...2510 days ago
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...2174 days ago
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...4011 days ago
2390 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...2261 days ago
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...3366 days ago
554 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...559 days ago