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  • Alignment program that allows the greatest number of mismatches

    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

  • #2
    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%

    Comment


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

      Comment


      • #4
        How long are the reads you want to align?
        ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

        Comment

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