Assembling 2x250 bp on 350 bp insert using SPAdes?

Question

[User 4014]

Hi folks,

I want to assembly a genome generated from HiSeq 2x250 bp with 350 bp insert size. I usually use SPAdes for assembly, but I just found out that SPAdes suggests using 550-700 bp fragments with 2x250 reads. May I ask if you have experience using SPAdes with 2x250 on 350 insert size? Is it just fine to use it or shall I use another tool?

Thanks in advance and have a great weekend!

[shenwei356]

I think that's ok, just try it.

[User 4014]

Hi Wei,

Thanks for your reply. I actually tried assembly and a little surprise by N50 of almost 150K. Perhaps I was paranoid. Anyway, I just got another library (150PE with 650 bp insert), but with much lower depth. I am now thinking to try merging the 250PE library and assembly it again with the new 150PE. I am not sure if SPAdes can handle one single read and one PE library, though. Do you have any suggestion?

Have a great weekend!

[shenwei356]

i didn't try this, but i think merging pe250 of 350 inserts is not necessary. i remember that spades can handel multiple libraries.