rm_chim - filter out chimeric reads based on alignment against a reference sequence
rm_chim [options] --fq raw_reads --db BWA_database
rm_chim aims to filter out chimeric reads that appear to be techinical artifacts related to certain library preparation protocols. It does this by the simplistic technique of mapping against a known reference sequence and removing reads for which subsequences map in opposite orientations against the genome.
IMPORTANT: Do not use this filter on data where genomic inversions might be expected to actually occur in yoru data.
Path to raw data in FASTQ format
Prefix of BWA database to map against. Either this or --fa must be specified.
Path to reference FASTA. Either this or --db must be specified.
Specify where to write passed reads to. Default: STDOUT.
Number of threads BWA should use. Default: 1.
Seed to pass to BWA (--k) (for deterministic mapping)
Minimum BWA alignment score to report (--T). Default: 20.
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Jeremy Volkening (jeremy.volkening@base2bio.com)
Copyright 2014-23 Jeremy Volkening
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.