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  • Comparison of NGS Alignment Projects

    Hi everyone,
    I'm starting a project to compare the various ngs alignment tools on the market for speed,accuracy, cpu consumption. Before I head down this path I 've found a few but enlightening papers on the subject but wanted some input from folks with a lot more experience in the field.

    I am thinking of taking a two prong approach. A layered analysis with increasing level of complexities. So the first 1/2 would be simulation data based on chromosome 16 hg19 reference sequence. Stick to one coverage but add sequencing errors, repeats, mismatches (1-3nt), and SNP introductions.

    I would then follow this by using real data from ENCODE. Something that has been published. Probably also using only one aligned chromosome.

    Tools:
    Simulation: (please suggest ones that can add repeats /multimaps)
    1. GemSIM
    2. samtools


    Alignment tools: (if I'm missing some please let me know)
    1. BWA
    2. Bowtie
    3. Novoalign
    4. SOAP
    5. ELAND
    6. RMAP
    7. SHRiMP
    8. MAQ


    Potential Metrics : (please add ones that you use or think would be useful)
    1. Really Mapped Genes (easier for Sim) is the core set of genes mapped by all alignment tools as true
    2. Negative mapped genes (unmapped): Total number of genes that were not mapped by any tool
    3. Comparisons between tools (mapped/unmapped)
    4. False Positives
    5. False Negatives
    6. MultiMap scoring


    I plan on doing some QC on each simulated read prior to running as a confirmation.

    Finally the tools will be available publicly and I may create some galaxy workflows. I 'd like this analysis to be useful to less technical people and to create a better decision tree for scientists to decide which tools are best for their applications.

    Thanks in advance and I hope others could help me fill in some of the gaps with their experience. Are there and simulation tools you use that would be good here? What alignment tools have I missed that you use? etc..

    Holes in my metrics or theory.

    Thanks,
    20
    BWA
    45.00%
    9
    Bowtie
    45.00%
    9
    Novoalign
    5.00%
    1
    SOAP (V1/2)
    0.00%
    0
    ELAND
    0.00%
    0
    RMAP
    0.00%
    0
    SHRiMP
    5.00%
    1
    MAQ
    0.00%
    0

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