User Tools

Site Tools


vsearch-software

vsearch

VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps.

Information

Usage

See versions of vsearch which are available:

$ module avail vsearch

Load one version into your environment and run it:

$ module load vsearch/2.8.0
$ vsearch

Installation

Notes from the sysadmin during installation:

$ wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-linux-x86_64.tar.gz
$ tar xf vsearch-2.8.0-linux-x86_64.tar.gz
$ sudo mkdir -p /export/apps/vsearch/2.8.0
$ sudo cp -r vsearch-2.8.0-linux-x86_64/* /export/apps/vsearch/2.8.0
$ sudo chmod 644 /export/apps/vsearch/2.8.0/man/vsearch.1
$ sudo chmod 644 /export/apps/vsearch/2.8.0/LICENSE* /export/apps/vsearch/2.8.0/README.md
$ sudo mkdir /export/apps/vsearch/2.8.0/man/man1
$ sudo mv /export/apps/vsearch/2.8.0/man/vsearch.1 /export/apps/vsearch/2.8.0/man/man1
vsearch-software.txt · Last modified: 2018/05/14 13:21 by aorth