A tool for mapping (short) DNA reads into reference sequences.
- 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 SAMTools output.
See README in the package for further information.
|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 SAMToolsrlcsa), and parallel searching (OpenMP). Alignment with mismatches (a hybrid algorithm or rotation indexes), or with mismatches and indels (suffix filters).|
|November 2012||Small bug fix (callcounter not reinitialized between reads)|
|April 2010||First public release (--gap and --mate-pair not yet implemented).|
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.