- Align reads using either k-mismatches or k-errors (mismatches, insertions and deletions) model; see README for different alignment modes.
- Algorithms are based on Burrows-Wheeler transform and backward backtracking, see the paper for details.
- Includes a novel data structure called the rotation index that finds alignments with higher number of mismatches in feasible time (but requires a larger index and fixed length query reads). Please see the paper for details.
- Supports FASTA and FASTQ input, and output.
See README in the package for further information.
News
| 2012-November |
A small bug fix: Callcounter not reinitialized between reads causing tail of the read set not mapped. |
| 2010-04-27 |
First public release: Supports FASTA and FASTQ input and rlcsa), and parallel searching (). Alignment with mismatches (a hybrid algorithm or rotation indexes), or with mismatches and indels (suffix filters). |
Downloads
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Small bug fix (callcounter not reinitialized between reads) |
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First public release (--gap and --mate-pair not yet implemented). |
References
V. Mäkinen, N. Välimäki, A. Laaksonen and R. Katainen: Unified View of Backward Backtracking in Short Read Mapping. To appear in Ukkonen Festschrift 2010 (Eds. Tapio Elomaa, Pekka Orponen, Heikki Mannila), Springer-Verlag, LNCS 6060, pp. 182-195, 2010.