<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43801?offset=630 https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads Tue, 28 Jan 2020 03:27:33 -0600 https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads <![CDATA[FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads]]> FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

http://bioinfo.ut.ee/FastGT/

https://github.com/bioinfo-ut/GenomeTester4/

Address of the bookmark: http://bioinfo.ut.ee/FastGT/

]]> 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/41362/genemates-an-r-package-for-detecting-horizontal-gene-co-transfer-between-bacteria-using-gene-gene-associations-controlled-for-population-structure Sat, 07 Mar 2020 05:52:20 -0600 https://bioinformaticsonline.com/bookmarks/view/41362/genemates-an-r-package-for-detecting-horizontal-gene-co-transfer-between-bacteria-using-gene-gene-associations-controlled-for-population-structure <![CDATA[GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure]]> GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where presence-absence status of acquired genes is usually confounded by bacterial population structure due to clonal reproduction.

https://www.biorxiv.org/content/10.1101/2020.02.29.970970v1

Address of the bookmark: https://github.com/wanyuac/GeneMates

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/40099/contiguator Fri, 04 Oct 2019 01:27:58 -0500 https://bioinformaticsonline.com/bookmarks/view/40099/contiguator <![CDATA[CONTIGuator !]]> CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

 

Address of the bookmark: https://sourceforge.net/projects/contiguator/

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