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  • Mapping bacterial genome with BWA - best seed length and algorithm?

    Hi There,

    I am mapping bacterial genomes to a reference sequence and am wondering if anyone has experience or knowledge with the best algorithm to use and/or any suggestion about seed length. (I'm new to bioinformatics!) Some of my samples are 95bp paired-end reads, and some are 115bp paired-end reads.

    Any suggestions on optimal parameters to use will be greatly appreciated! (Note: I have trimmed the sequences.)

  • #2
    Mapping bacterial genome with BWA - best seed length and algorithm?

    The popular short-read aligners BWA and Bowtie/Bowtie2 should work fine if you have a reference genome. Just use the default parameters in the first instance.

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    • #3
      @mrood

      Check out these alignment benchmarks for some different popular tools (BWA, Bowtie2, Novoalign) here:





      As for parameters, default parameters should be fine with any of those. Personally, I would recommend BWA-MEM as it is fast and accurate for those read lengths.

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      • #4
        Thank you mastal and oiiio!

        I previously mapped with the bwa aln sampe and I have tried the bwa mem on one sample. From a quick comparison by eye in IGV it looks like the bwa mem will work better for my samples. I forgot to mention that they are pooled samples, so proper mapping is very critical for downstream analyses.

        I appreciate both of your fast responses!

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