Align full length contigs instead of reads

[sagnikbanerjee15]

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

[GenoMax]

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.

[sagnikbanerjee15]

Thanks a lot!!! You were of immense help

[gringer]

LAST and GraphMap should also work.

[sagnikbanerjee15]

LAST and GraphMap should also work.

Thank you. David