<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37666?offset=40 https://bioinformaticsonline.com/bookmarks/view/41397/svaba-structural-variation-and-indel-detection-by-local-assembly Tue, 10 Mar 2020 07:52:15 -0500 https://bioinformaticsonline.com/bookmarks/view/41397/svaba-structural-variation-and-indel-detection-by-local-assembly <![CDATA[SvABA: Structural variation and indel detection by local assembly]]> SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26543/breakseq2 Mon, 29 Feb 2016 17:45:38 -0600 https://bioinformaticsonline.com/bookmarks/view/26543/breakseq2 <![CDATA[BreakSeq2]]> Ultrafast and accurate nucleotide-resolution analysis of structural variants

More at http://bioinform.github.io/breakseq2/

Download BreakSeq2

Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gz

For other versions, see "releases". https://github.com/bioinform/breakseq2/releases

Address of the bookmark: http://bioinform.github.io/breakseq2/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/29912/maq-mapping-and-assembly-with-quality Tue, 22 Nov 2016 04:51:39 -0600 https://bioinformaticsonline.com/bookmarks/view/29912/maq-mapping-and-assembly-with-quality <![CDATA[Maq: Mapping and Assembly with Quality]]> Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/. Maq is previously known as mapass2.

Run Maq Now

Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.

  1. Prepare a reference sequence (ref.fasta). Better a bacterial genome.
  2. Download maq, maq-data and maqview at the download page.
  3. Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.
  4. Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go: 
    maq.pl demo ref.fasta calib-30.dat
    where calib-30.dat is contained in maq-data.
  5. View the alignment: 
    cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.

Address of the bookmark: http://maq.sourceforge.net

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