<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41300?offset=490 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/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Wed, 06 Oct 2021 07:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments Mon, 22 Sep 2025 23:51:02 -0500 https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments <![CDATA[Termal: a fast and interactive terminal-based viewer for multiple sequence alignments]]> termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

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