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Align full length contigs instead of reads

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  • Align full length contigs instead of reads

    Hello,

    Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available. I wish to align those contigs to the genomes. Do you think using HiSAT2 and STAR to align the contigs to a long genome will be a good choice? If not, could anyone suggest a better alternative?

    Thank you

  • #2
    You could use mapPacBio.sh from BBMap (which chunks input sequences into 6 kb pieces and then aligns them).

    In this size range though you could use BLAT or LASTZ as other alternatives.

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    • #3
      Thanks a lot!!! You were of immense help

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      • #4
        LAST and GraphMap should also work.

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        • #5
          Originally posted by gringer View Post
          LAST and GraphMap should also work.
          Thank you. David

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