PRINSEQ
=======

PReprocessing and INformation of SEQuence data (http://prinseq.sourceforge.net)

PRINSEQ will help you to preprocess your genomic or metagenomic sequence data in
FASTA or FASTQ format.


LITE VERSION
------------

The lite version is a standalone perl script (prinseq-lite.pl) that does not
require any non-core perl modules for processing.

The used modules are:

   Getopt::Long
   Pod::Usage
   File::Temp qw(tempfile)
   Fcntl qw(:flock SEEK_END)
   Digest::MD5 qw(md5_hex)
   Cwd
   List::Util qw(sum min max)

To run the lite version, you can either use "perl prinseq-lite.pl [options]" or
rename the "prinseq-lite.pl" into "prinseq-lite", add the execution mode
("chmod +x prinseq-lite") and use "prinseq-lite [options]".

The available options are processed in the following order: seq_num, trim_left,
trim_right, trim_left_p, trim_right_p, trim_qual_left, trim_qual_right,
trim_tail_left, trim_tail_right, trim_ns_left, trim_ns_right, trim_to_len,
min_len, max_len, range_len, min_qual_score, max_qual_score, min_qual_mean,
max_qual_mean, min_gc, max_gc, range_gc, ns_max_p, ns_max_n, noniupac,
lc_method, derep, seq_id, seq_case, dna_rna, out_format


GRAPHS VERSION
--------------

The graphs version is a standalone perl script (prinseq-graphs.pl) that
generates graphs and HTML report files. The input is generated by the lite
version.

The used modules are:

   Getopt::Long
   Pod::Usage
   File::Temp qw(tempfile)
   Fcntl qw(:flock SEEK_END)
   Cwd
   JSON
   Cairo
   Statistics::PCA
   MIME::Base64

Due to issues with the Statistics::PCA module on certain platforms, a graphs
version without this module is additionally provided (prinseq-graphs-noPCA.pl).

To run the graphs version, you can either use "perl prinseq-graphs.pl [options]"
or rename the "prinseq-graphs.pl" into "prinseq-graphs", add the execution mode
("chmod +x prinseq-graphs") and use "prinseq-graphs [options]".

If you have trouble installing the required modules or want to see an output
example report, upload the graph data file at:
http://edwards.sdsu.edu/prinseq -> Choose "Get Report"


WEB VERSION - DEPENDENCIES
--------------------------

The PERL scripts require these modules:

   CGI
   JSON
   File::Temp
   Digest::MD5
   Fcntl
   Cairo
   Statistics::PCA
   IO::Uncompress::AnyUncompress


BUG REPORTS
-----------

If you find a bug please email me at <rschmieder_at_gmail_dot_com> so that I can
make PRINSEQ better.


MAILING LIST
------------

If you want to receive emails for new releases and updates, please sign up for
the mailing list at https://lists.sourceforge.net/lists/listinfo/prinseq-news


COPYRIGHT AND LICENSE
---------------------

Copyright (C) 2010-2013  Robert SCHMIEDER

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/>.