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is there an Mappers/aligners working on adam sequencing data

i'm trying to use adam to speedup the alignment & mapping process of fastq sequence data?

currently we are using bwa to do that ,which is very very slow.

is there an Mappers/aligners working on adam sequencing data to speed up the alignment?

gene sequence alignment rna-seq
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updated by zhangnew • zhangnew • written by inred9 • inred9

Who is Adam? Does he have a Facebook page or any other info? :)

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written by John John

Wow, a whole huge suite of tools i've never seen before! Awesome! I should read up on this... thanks inred9 and WorcesterShireSaucer ;-) :)

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written by John John

When you say "slow", is it because the alignment itself is slow, or because conversion to fastq is slow? If it is former, use SNAP; if latter, you should stream fastq to the mapper – most mainstream mappers can read fastq from stdin – instead of writing the actual fastq to disk.

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written by lh3 lh3

snap is in beta version, but I'll give it try and check the difference

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written by inred9 • inred9

1 answer

Did you try bgzip format fastq work with Cannoli ？

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written by zhangnew • zhangnew

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