I appreciate hearing about your experience with the program.
FastqSifter accepts a FASTA sequence (e.g., mitochondrial genome sequence), will align a set of reads (left, right, and optionally unpaired) to this sequence using bwa, then remove reads that align from the original set of reads, and optionally save the aligned reads to a separate FASTQ file.
https://github.com/josephryan/FastqSifter (click the "Download ZIP" button at the bottom of the right column).
General system tools:
- [Perl] (http://www.cpan.org/), comes with most operating systems
- JFR-PerlModules - https://github.com/josephryan/JFR-PerlModules
- This is currently the only aligner that works with FastqSifter
FastqSifter and documentation, type the following:
perl Makefile.PL make sudo make install
If you do not have permission to install to the system see the following:
FastqSifter --out=PREFIX_FOR_OUTFILES --fasta=CONTAM_FASTA --left=LEFT_FASTQ --right=RIGHT_FASTQ [--threads=NUM_THREADS] [--unp=UNPAIRED_FASTQ] [--savereads] [--version] [--help]
Documentation is embedded inside of
FastqSifter in POD format and
can be viewed by running any of the following:
FastqSifter --help perldoc FastqSifter man FastqSifter # available after installation
COPYRIGHT AND LICENSE
Copyright (C) 2015 Joseph F. Ryan
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 in the file LICENSE. If not, see http://www.gnu.org/licenses/.