<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37493?offset=20 https://bioinformaticsonline.com/bookmarks/view/27090/canu-assembling-large-genomes-with-single-molecule-sequencing-and-locality-sensitive-hashing Tue, 26 Apr 2016 11:38:10 -0500 https://bioinformaticsonline.com/bookmarks/view/27090/canu-assembling-large-genomes-with-single-molecule-sequencing-and-locality-sensitive-hashing <![CDATA[CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.]]> Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Canu is a hierachical assembly pipeline which runs in four steps:

  • Detect overlaps in high-noise sequences using MHAP
  • Generate corrected sequence consensus
  • Trim corrected sequences
  • Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43870/quip-aggressive-compression-of-fastq-sam-and-bam-files Tue, 24 May 2022 06:31:48 -0500 https://bioinformaticsonline.com/bookmarks/view/43870/quip-aggressive-compression-of-fastq-sam-and-bam-files <![CDATA[Quip: Aggressive compression of FASTQ, SAM and BAM files.]]> This will help us to reduce the amount of drive space we take up and decrease data transfer times

Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size.

Address of the bookmark: https://github.com/dcjones/quip

]]> Neel https://bioinformaticsonline.com/file/view/45346/when-ngs-gives-you-more-data-than-you-ever-asked-for Wed, 23 Sep 2026 10:16:43 -0500 https://bioinformaticsonline.com/file/view/45346/when-ngs-gives-you-more-data-than-you-ever-asked-for <![CDATA[When NGS gives you more data than you ever asked for!]]>

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43957/gfastats-the-swiss-army-knife-for-genome-assembly Thu, 08 Sep 2022 06:03:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43957/gfastats-the-swiss-army-knife-for-genome-assembly <![CDATA[gfastats: The swiss army knife for genome assembly.]]> gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.

Address of the bookmark: https://github.com/vgl-hub/gfastats

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/29500/genomescope-open-source-web-tool-to-rapidly-estimate-the-overall-characteristics-of-a-genome-including-genome-size-heterozygosity-rate-and-repeat-content-from-unprocessed-short-reads Fri, 21 Oct 2016 05:46:43 -0500 https://bioinformaticsonline.com/bookmarks/view/29500/genomescope-open-source-web-tool-to-rapidly-estimate-the-overall-characteristics-of-a-genome-including-genome-size-heterozygosity-rate-and-repeat-content-from-unprocessed-short-reads <![CDATA[GenomeScope: open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads]]>

Summary: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels, and error rates. Availability and Implementation: http://qb.cshl.edu/genomescope/, https://github.com/schatzlab/genomescope.git

Address of the bookmark: http://qb.cshl.edu/genomescope/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs Fri, 04 Nov 2016 10:48:00 -0500 https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs <![CDATA[R Graphs !!]]> The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided. Enjoy nice graphs !!

Address of the bookmark: http://rgraphgallery.blogspot.be/

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