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-   -   Align full length contigs instead of reads (http://seqanswers.com/forums/showthread.php?t=76391)

sagnikbanerjee15 06-04-2017 10:15 AM

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

GenoMax 06-04-2017 05:08 PM

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 06-04-2017 05:36 PM

Thanks a lot!!! You were of immense help

gringer 06-04-2017 08:01 PM

LAST and GraphMap should also work.

sagnikbanerjee15 06-04-2017 08:16 PM

Quote:

Originally Posted by gringer (Post 208107)
LAST and GraphMap should also work.

Thank you. David


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