align.multifastas.parallel.sh

Description

Align multi-sequence FASTA files for a batch of target regions in parallel.

Usage

align.multifastas.parallel.sh -d <directory> -m <string> -t <positive integer>

Dependencies

mafft

Arguments

# Required
-d                Path to directory with multifasta files. This directory should contain a FASTA file for each
                  target region, each with unaligned contigs of multiple samples.

# Optional [DEFAULT]
-m [`localpair`]  MAFFT alignment model. Choose between 'localpair', 'globalpair' or 'genafpair'.
                  See MAFFT documentation for further details.
-t         [4]    Number of parallel threads.

Details

Value

This script creates an output directory of the form mafft.${nind}.${nloc}, where ${nind} is the number of samples and ${nloc} is the number of loci.

Examples

align.multifastas.parallel.sh -d multifasta.63.2396 -m 'localpair' -t 20