<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38445?offset=100 https://bioinformaticsonline.com/bookmarks/view/42160/vicuna-a-software-tool-that-enables-consensus-assembly-of-ultra-deep-sequence-derived-from-diverse-viral-or-other-heterogeneous-populations Tue, 25 Aug 2020 03:40:17 -0500 https://bioinformaticsonline.com/bookmarks/view/42160/vicuna-a-software-tool-that-enables-consensus-assembly-of-ultra-deep-sequence-derived-from-diverse-viral-or-other-heterogeneous-populations <![CDATA[VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.]]> VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.

http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf

Address of the bookmark: https://www.broadinstitute.org/viral-genomics/vicuna

]]> biogeek https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies Sat, 11 Sep 2021 00:28:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies <![CDATA[RagTag: a collection of software tools for scaffolding and improving modern genome assemblies]]> RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Address of the bookmark: https://github.com/malonge/RagTag

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment Wed, 21 Feb 2024 15:01:20 -0600 https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment <![CDATA[OMArk: software for proteome (protein-coding gene repertoire) quality assessment]]> OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families.

Address of the bookmark: https://github.com/DessimozLab/OMArk

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