create.multifastas.parallel.sh

Description

Create multi-sequence FASTA files uf unaligned contigs, for a batch of target regions in parallel.

Usage

create.multifastas.parallel.sh -s <file> -l <file> -d <directory> -t <positive integer>

Dependencies

Arguments

# Required
-s        Path to file with sample basenames (without header or '>').
-l        Path to file with locus names (without header or '>').
-d        Path to directory with exonerate results. This directory should contain a subdirectory for each sample,
          with FASTA files with the best-matching contigs.

# Optional [DEFAULT]
-t  [15]  Number of alignments processed in parallel.

Details

Value

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

Examples

create.multifastas.parallel.sh -s samlples.txt -l loci.txt -d NovaSeq-run1_exonerate -t 20