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  • #1

    Indexing with bfast

    Hi

    I'm starting to use bfast and I have some doubts about some indexing parameters.

    When indexing do I have to do it with the 10 spaced seed? I know this is to create different indexes to find the best CAL.

    Which number should I use for -w parameter and why?


    This is an example. Should it be run such way? 10 times? Can it be runed less than 10 times? Is it fixed (I mean it can be runned at a maximum of 10 times with the prefixed -m I show below or I could run it 11 times being the 11th such like '10001')

    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111111111111111111111" -w 14 -i 1
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111110111011101010010101101111" -w 14 -i 2
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1011110101101001011000011010001111111" -w 14 -i 3
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "10111001101001100100111101010001011111" -w 14 -i 4
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11111011011101111011111111" -w 14 -i 5
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111111100101001000101111101110111" -w 14 -i 6
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11110101110010100010101101010111111" -w 14 -i 7
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111101101011011001100000101101001011101" -w 14 -i 8
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111011010001000110101100101100110100111" -w 14 -i 9
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111010010110110101110010110111011" -w 14 -i 10
    Thanks for your time.
    Last edited by runnerBio88; 12-11-2015, 01:58 AM.
    Tags: bfast, index, mask, seed
  • #2
    Well, I have seen that most of my doubts are explained not in the manual but in the paper.
    BFAST: An Alignment Tool for Large Scale Genome Resequencing
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007767
    Background The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25–100 base range, in the presence of errors and true biological variation. Methodology We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. Conclusions We compare BFAST to a selection of large-scale alignment tools - BLAT, MAQ, SHRiMP, and SOAP - in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at http://bfast.sourceforge.net.

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