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Old 06-04-2017, 09:15 AM   #1
sagnikbanerjee15
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Default 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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Old 06-04-2017, 04:08 PM   #2
GenoMax
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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.
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Old 06-04-2017, 04:36 PM   #3
sagnikbanerjee15
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Thanks a lot!!! You were of immense help
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Old 06-04-2017, 07:01 PM   #4
gringer
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LAST and GraphMap should also work.
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Old 06-04-2017, 07:16 PM   #5
sagnikbanerjee15
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Quote:
Originally Posted by gringer View Post
LAST and GraphMap should also work.
Thank you. David
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