Alignment program that allows the greatest number of mismatches

[CarlHSLee]

I am trying to align reads allowing for as many mismatches as possible. I was using Novocraft before and that program allows me to align up to about 9 mismatches. Is there a program out there that can allow more?

thanks

[dietmar13]

Stampy?

As far as I know Stampy is not restricted to a specific number of mismatches...

http://www.well.ox.ac.uk/project-stampy

Stampy has the following features:

- Maps single, paired-end, mate pair Illumina reads to a reference
- Fast: about 10 (with BWA) or 15 hours (without) per Gbase
- Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome
- High sensitivity for indels and divergent reads, up to 10-15%
- Low mapping bias for reads with SNPs or indels
- Well calibrated mapping quality scores
- Input: Fastq and Fasta; gzipped or plain; SAM and BAM
- Output: SAM, Maq's map file
- Optionally calculates per-base alignment posteriors
- Optionally processes part of the input
- Handles reads up to 4500 bases

To calculate correct mapping qualities, Stampy needs to know the
expected divergence from the reference. This is set with the
--substitutionrate= option. The default is 0.001 substitutions per
site.

Increasing the read length, and using paired-end reads, helps mapping
divergent reads. The following table gives an indication of the
divergence at which a reasonable proportion of reads can be correctly
mapped. These numbers were obtained by simulation, using the human
genome as reference, and should be taken as an indication only; they
are dependent on error rates, the repetitiveness of the genome, the
insert size distribution, and local variations in divergence; in
addition no indel mutations were included.

36bp 36bp 72bp 72bp
divergence | single paired single paired
-------------------------------------------------------
0% | 82% 95% 87% 96%
3% | 73% 91% 80% 94%
6% | 60% 83% 72% 92%
9% | 41% 56% 56% 88%
12% | 28% 51% 48% 80%

[HESmith]

BFAST does a better job than most aligners (Figure 3 of the paper shows comparative analysis), although I don't believe Stampy was included.

[ecSeq Bioinformatics]

How long are the reads you want to align?