ASAP - Allele-specific alignment pipeline
| Function | A tool to determine genome-specific alignments for high-throughput sequencing experiments |
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| 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.
- Alignments against two genomes in a single step
- Supports single-end and paired-end read alignments of variable length
- Alignment seed length, number of mismatches, insert size etc. are adjustable
- Individual output files for genome 1- or genome 2-specific alignments and alignments in common
Changelog
- 09-01-12: Version 0.1.2 released
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- Added an extra check for single-end and paired-end files which prevents error messages when a chromosome is not present in equivalent genomes (e.g. if one genome does not have MT as a chromosome)
- Removed the requirement of paired-end sequences to have identical sequence IDs
- Increased the 'chunkmbs' default value to 512 MB
- Fixed a counting bug for --dissimilar alignment mode where sequences aligning equally well to both genomes were counted for "multiple alignments to the same genome" instead of "aligning equally well to both dissimilar genomes". This should now work as intended in both single-end and paired-end mode
- 16-08-11: Version 0.1.1 released
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- Increased the 'chunkmbs' default value to 256 MB (up from 64 MB)
- ASAP will now accept single-end files in both comma and space separated format
- 07-07-11: Version 0.1.0 released
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- Initial release
- All basic functions working