Combining multiple libraries about gatb-minia-pipeline HOT 5 CLOSED

Hi! Apologies for the delayed answer. Indeed the FOF strategy doesn't work as is.
You'll need to

1. if applicable, for each insert size, concatenate all the left (resp. right) files from that insert size into a single left (resp. right) file
2. pass as argument each insert size library, e.g. -1 left_insertA.fq.gz -2 right_insertA.gz --mp-1 left_insertB.fq.gz --mp-2 right_insertB.fq.gz in order from smaller insert size to larger (ie in my example, insert size A is smaller than B)

Alternatively:

1. run gatb-pipeline a FOF of all libraries in any order. This will produce contigs but no scaffold. Note that these will be the same contigs as if you had specified that librairies were paired/mate-pairs, as Minia does not care about pairing when making contigs. Then you can run BESST stand-alone (using the gatb-pipeline script by using the -c argument, or just the BESST program, or any other scaffolder) manually using the contigs produced by gatb-pipeline.

from gatb-minia-pipeline.

Thank you for the suggestion and apologies for the delayed response!

I did use a mixture of the two options though. I concatenated the smaller insert fastqs and used the mate-pair separately.

from gatb-minia-pipeline.

sounds good, did it work?

from gatb-minia-pipeline.

Yup, it did! I got a decent contiguity as well.

Got the 2.5Gb genome in 9876 (no joke) scaffolds over 1kb in length with an N50 of 1.83Mb. Having a 8Kb and 20Kb insert MP libraries did help a lot combined with dual scaffolding.

from gatb-minia-pipeline.

very nice!

from gatb-minia-pipeline.