Align full length contigs instead of reads

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sagnikbanerjee15

Junior Member

Join Date: Jun 2017

Posts: 3
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#1

Align full length contigs instead of reads

06-04-2017, 09:15 AM

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
Tags: align, contigs, hisat2, short reads, star
GenoMax

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Join Date: Feb 2008

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#2

06-04-2017, 04:08 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.
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sagnikbanerjee15

Junior Member

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#3

06-04-2017, 04:36 PM

Thanks a lot!!! You were of immense help
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gringer

David Eccles (gringer)

Join Date: May 2011

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#4

06-04-2017, 07:01 PM

LAST and GraphMap should also work.
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sagnikbanerjee15

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#5

06-04-2017, 07:16 PM

Originally posted by gringer View Post

LAST and GraphMap should also work.

Thank you. David
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