VSEARCH

Overview

VSEARCH: The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). … We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

• Documentation:

• The Bioinformatics v3.0 article from UW’s Genome Technologies Laboratory is an extensive article on using vsearch and related applications.

Using

Use the module name vsearch to discover versions available and to load the application.

Run vsearch --help from the command-line to view all the available commands that it offers and options available.

Multicore

View the vsearch help for further details of the general --threads option.