Originally posted by gringer
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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.Leave a comment:
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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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