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Old 06-16-2008, 06:13 AM   #1
Senior Member
Location: Kuala Lumpur, Malaysia

Join Date: Mar 2008
Posts: 126
Default New Short Read Aligner

I've been working on a short read aligner and would like to find some beta testers. The suite includes single end and paired end read aligners.
Some features are:
  • Gaps up to 7bp, affine gap penalties
  • Can handle ambiguous codes in ref sequence.
  • Quality based scoring
  • Adapter stripping for miRNA reads
  • No heuristics - reports the best alignment
  • Options for handling multiple alignments includes none, random, all alignments.
  • Alignment Quality scores
  • Can use fasta, fastq, solexa fastq, prb input formats
  • Paired end with full Needleman-Wunsch on both ends.
  • Paired end accepts a structural variation penalty and the best alignment may be two independent ends if score with SV penalty is better than the best pair that fits the fragment length distribution.
  • Supports variable read lengths
  • Includes optional soft masking of repeats.

If anyone is interested in getting a copy for testing you can contact me novoalign <at> gmail ....
Beta version is for X86-64 Linux 64 bit.

Cheers, Colin

Last edited by sparks; 06-17-2008 at 12:51 AM.
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