PARA-suite aligner

PAR-CLIP Analyzing suite. Based on the implementation of the Burrows-Wheeler Aligner (BWA; aln/samse/sampe algorithm) Version 0.7.8 and extends it with the use of an empirical error profile.

Installation

git clone https://github.com/akloetgen/PARA-suite_aligner.git
cd PARA-suite_aligner
make

For an easy use of the PARA-suite ailgner we recommend the additional download of the PARA-suite, wrapping the PARA-suite aligner into a best-practice pipeline for read mapping (https://github.com/akloetgen/PARA-suite)

Usage

./bwa parasuite [options] <reference_fasta> <input>

Help

./bwa parasuite

Example on testdata

./bwa index examples/reference_chr1.fa
./bwa parasuite -p examples/reference_chr1.errorprofile -f examples/testout_simulation_mapped_PARMA.sai examples/reference_chr1.fa examples/testout_simulation.fastq
./bwa samse examples/reference_chr1.fa examples/testout_simulation_mapped_PARMA.sai examples/testout_simulation.fastq > examples/testout_simulation_mapped_PARMA.sam