Compute all pairwise (global) alignments with VSEARCH

This function is a wrapper function to compute all pairwise (global) alignments using VSEARCH.

AllPairwiseAlign(
  file,
  cores = 1,
  mask = "none",
  out.name = "AllPairwiseAlign",
  output = NULL
)

Arguments

file	path to fasta file storing sequences for which all possible pairwise alignments shall be computed.
cores	number of cores that shall be used for parallel computations.
mask	shall the aligned sequences be maksed? Options are: `mask = "none"`, `mask = "dust"`, `mask = "soft"`.
out.name	name of the output files (`.uc`, `_userout.txt`, `.blast6out`), `_fasta_pairs.fasta`, `*.sam`.
output	path to a folder in which output shall be stored.

A folder named vsearch_pairwise_align will be created and the following files will be stored in this output folder:

*.uc USEARCH cluster format generated by VSEARCH storing the sequence cluster information of aligned sequences.
*_userout.txt a tab separated file storing the alignment information in the columns: query, target, sequence identity (ID).
*.blast6out BLAST output format of the pairwise (global) sequence alignments generated by VSEARCH.
*_fasta_pairs.fasta fasta file storing the alignments.
*.sam SAM file storing the alignments.

To be able to use this function the VSEARCH command line tool needs to be installed.

https://github.com/torognes/vsearch

Hajk-Georg Drost