frag_lens - Calculate paired end fragment lengths from read alignment
frag_lens [--sam <in.sam>] OR [--ref <cons.fa> --forward <R1.fq> --reverse <R2.fq>] [options] > frag_lens.txt
Calculates library fragment lengths based on paired-end read alignment. Takes as input either a preprepared SAM alignment or a reference and read files from which it produces an alignment. Outputs calculated fragment lengths, one per line.
Requires the following binaries:
Path to input SAM alignment.
Path to reference sequence (e.g. assembly)
Forward reads in FASTQ format
Reverse reads in FASTQ format
Maximum number of alignment records to read as input. Used to limit run times.
Number of threads to use for alignment (ignored if --sam is given)
Please submit bug reports to the issue tracker in the distribution repository.
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/>.