<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27713?offset=1330 https://bioinformaticsonline.com/bookmarks/view/29276/murasaki Fri, 30 Sep 2016 10:22:30 -0500 https://bioinformaticsonline.com/bookmarks/view/29276/murasaki <![CDATA[Murasaki]]> Murasaki is an anchor alignment program that is

  • exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
  • scalable (Arbitrarily parallelizable across multiple nodes using MPI)
  • memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
  • unlimited by pattern length or selection
  • repeat tolerant

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Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics Tue, 04 Oct 2016 14:50:48 -0500 https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics <![CDATA[MIRO : miRNA omics]]> The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

]]> Jit 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/29578/plink2 Thu, 27 Oct 2016 11:24:45 -0500 https://bioinformaticsonline.com/bookmarks/view/29578/plink2 <![CDATA[PLINK2]]> This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others. (What's new?) (Credits.) (Methods paper.)

Address of the bookmark: https://www.cog-genomics.org/plink2/

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