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ASAP - Allele-specific alignment pipeline

Function A tool to determine genome-specific alignments for high-throughput sequencing experiments
Language Perl
Requirements A functional version of Bowtie is required.
Code Maturity Stable. ASAP has been successfully used for different applications and genomes.
Code Released Yes, under GNU GPL v3 or later.
Initial Contact Felix Krueger

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Heterozygous differences in a sequencing sample can be detected by aligning reads to a reference genome and identifying allele-specific events from a SNP pileup file. However, this introduces a bias in favour of the reference allele. ASAP analyses allelic differences in NGS data in a less biased way by aligning sequences to two reference genomes in parallel using the short-read aligner Bowtie. ASAP produces three different output files, two for genome-specific alignments as well as one for alignments which both genomes have in common.