AmpliconClipper

AmpliconClipper performes post-alignment PCR Primer removal. In a multitude of situations, pre-alignment clipping is not feasible; either because the primers themselves become progressively shorter or the sequencing platform is rather noisy (AmpliconClipper was designed with Pacific Biosciences data in mind).

Features

• Takes SAM as input
• Can specify either primers or amplicons directly
• Can specify whether forward resp. reverse reads can only come from specific amplicons
• Can discard reads with a below fraction coverage of an amplicon

PREREQUISITES TO BUILD:

• You will require a C++ compiler that can handle C++98

Building:

git clone git://github.com/SoapZA/AmpliconClipper.git;
cd AmpliconClipper;
make;

Running:

See the helptext:

AmpliconClipper
         by David Seifert 2013

Options:
         -i   : input SAM file
         -o   : output SAM file
         -a   : input amplicon file
         -S   : (optional) write statistics of reads
         -I   : (optional) maximum insertions threshold
         -D   : (optional) maximum deletions threshold
         -C   : (optional) minimum coverage threshold as a fraction of the amplicon insert
        --mD  : (optional) maximum adjacent deletions
        --ref : required if you provide a list of primers. Amplicons are found by locating primers on the reference genome.

Specifying amplicons:

In order to specify amplicons, you have two options:

• Either provide a file with the start, end, start of the insert and end of the insert of the amplicon. Additionally, specify in which direction reads can originate from this amplicon, i.e. '+' for this amplicon only yielding reads in the forward (sense) direction and '-' for reads in the anti-sense direction. Provide '0' if both sense and anti-sense reads can originate from this amplicon. The last column can contain a capital 'X', such that reads from this amplicon are discarded.
• You can also give AmpliconClipper a FASTA file with primers. Every FASTA ID should occur not more or less than twice and AmpliconClipper will locate all amplicon parameters by searching the reference genome.

LICENSE:

GNU GPLv3 http://www.gnu.org/licenses/gpl-3.0