is there an Mappers/aligners working on adam sequencing data

Question

[inred9]

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?

[John]

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

[WouterDeCoster]

RTFB! (Read The Fucking Bible)

[inred9]

ADAM is a genomics analysis platform with specialized file formats designed to scale well to large datasets. it can Convert fastq/sam/bam to adam format or vise versa

https://github.com/bigdatagenomics/adam

[John]

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

[lh3]

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.

[inred9]

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

Answer 1

[zhangnew]

Did you try bgzip format fastq work with Cannoli ？