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Align full length contigs instead of reads

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  • sagnikbanerjee15
    replied
    Originally posted by gringer View Post
    LAST and GraphMap should also work.
    Thank you. David

    Leave a comment:


  • gringer
    replied
    LAST and GraphMap should also work.

    Leave a comment:


  • sagnikbanerjee15
    replied
    Thanks a lot!!! You were of immense help

    Leave a comment:


  • GenoMax
    replied
    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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  • 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
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