Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
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FastqSifter
LICENSE
Makefile.PL
README.md

README.md

FastqSifter

DESCRIPTION

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.

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AVAILABILITY

https://github.com/josephryan/FastqSifter (click the "Download ZIP" button at the bottom of the right column).

DEPENDENCIES

General system tools:

Additional package

BWA

INSTALLATION

To install 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:

http://www.perlmonks.org/index.pl?node_id=128077#permission

RUN

FastqSifter --out=PREFIX_FOR_OUTFILES --fasta=CONTAM_FASTA
   --left=LEFT_FASTQ --right=RIGHT_FASTQ [--threads=NUM_THREADS]
   [--unp=UNPAIRED_FASTQ] [--savereads] [--version] [--help]

DOCUMENTATION

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/.