<![CDATA[BOL: fragScaff: Genome Assembly with Contiguity Preserving Transposition]]> https://bioinformaticsonline.com/bookmarks/view/36594/fragscaff-genome-assembly-with-contiguity-preserving-transposition? https://bioinformaticsonline.com/bookmarks/view/36594/fragscaff-genome-assembly-with-contiguity-preserving-transposition Mon, 14 May 2018 04:28:14 -0500 https://bioinformaticsonline.com/bookmarks/view/36594/fragscaff-genome-assembly-with-contiguity-preserving-transposition <![CDATA[fragScaff: Genome Assembly with Contiguity Preserving Transposition]]> Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files.

Manuscript describing fragScaff was published as: Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.

 

Address of the bookmark: https://sourceforge.net/projects/fragscaff/files/

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