Question: Assembling 2x250 bp on 350 bp insert using SPAdes?
0
gravatar for User 4014
2.5 years ago by
User 401430
Sweden
User 401430 wrote:

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!

next-gen assembly genome • 794 views
ADD COMMENTlink written 2.5 years ago by User 401430

I think that's ok, just try it.

ADD REPLYlink written 2.5 years ago by shenwei3564.8k

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!

ADD REPLYlink written 2.5 years ago by User 401430

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

ADD REPLYlink written 2.5 years ago by shenwei3564.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1327 users visited in the last hour