How long time it typical takes to do a alignment on a human chromosome fastq file?

Question

[jasonlee6728]

Have someone every done a alignment job on human chromsome fastq files? Please tell me the software you use, the time it cost and also some computer hardware details. Thanks a lot!

Answer 1

[Asaf]

There is a comparison of STAR, Tophat2, RUM, MapSplice, GSNAP in table 1 of the STAR paper:

STAR: ultrafast universal RNA-seq aligner

Answer 2

[Thibault D.]

Hi,

As you said, this amount of time is directly related to (1) the size of your fastq files, (2) the software you will use, and (3) the hardware your work environment relies on.

I think the amount of time should not be the only thing to watch : sometimes a reduced amount of RAM requirements allows you to perform multiple single-alignments at the same time. One by one, each run takes more time, but in fine the global amount of time is reduced.

Usually, tools that requires less RAM, also requires more computing time. There are (of course!) exceptions.

IMHO, STAR and CRAC2 (not the version 1) are good candidates, for quick and effective human alignments.

[michael.ante]

I also like STAR a lot, but it needs quite some memory (30 Gig +).
Depending on whether it's RNA-Seq or DNA-Seq different aligners should be used.
Additionally, don't underestimate the time of building the index.