Pamir: Insertion Discovery Tool for Whole Genome Sequencing Data

Pamir is a computational tool for detecting novel sequence insertions in single or multiple paired-end WGS(Whole Genome Sequencing) Illumina reads based on orphans and one-end anchors (OEA).

Prerequisities and Compilation

Pamir relies on specific version of the following tools:

g++ 4.9.0 or higher

Python 2.7 or higher (needed for the package argparse )

boost library 1.62 or higher

You also need to define the boost library by typing on your shell
export BOOST_INCLUDE= the/BOOST/version/include/ (directory of BOOST in your machine).

velvet 1.2.10 or higher

BLAST 2.3.0+ or higher

Latest BLAST nt database is also needed to be downloaded in dir/to/blast/db (needed for contamination detection).
mkdir dir/to/blast/db
cd dir/to/blast/db
../bin/update nt

Then, just clone our repository:

git clone --recursive
cd pamir

You need to update pamir.config in pamir folder with your paths for the binaries samtools, velveth, velvetg, blastn and the blast database folder db:

vim pamir.config
Write your paths for the binaries:

Then make

pamir$ make

How do I run Pamir?

You can use either of these commands:

pamir$ ./ -h
pamir$ python -h

to get a description of each parameter. For more details, please check doc/pamir_manual.pdf.

Contact & Support

Feel free to drop any inquiry to pinarkavak at gmail dot com.