Question: SPADES contig output
0
gravatar for las996
7 months ago by
las9960
las9960 wrote:

Hi everyone, I'm using SPAdes 3.12 to assemble contigs using reads. The question is, is there any way to retrieve the reads used to assemble the contigs without a further alignment step? I believe that if SPAdes build the contigs using the reads it must containg this information somewhere I could not find. Thank you in advance!

assembly • 247 views
ADD COMMENTlink modified 7 months ago by h.mon29k • written 7 months ago by las9960
2

no, not as far as I know.

SPAdes uses bwa to align the reads back, so you'll have to go that way, too. There used to be a bwa binary with distributed spades

ADD REPLYlink written 7 months ago by Carambakaracho1.9k

I'll try to contact them, thank you.

ADD REPLYlink written 7 months ago by las9960
1
gravatar for h.mon
7 months ago by
h.mon29k
Brazil
h.mon29k wrote:

As Carambakaracho said, I don't think SPAdes saves this information of which reads used to assemble the contigs - ask the SPAdes developers to be certain, they are generally very responsive.

Note that mapping is not the same as assembling, and reads mapping to a contig don't necessarily mean these reads were used to assembly the contig - it should be a good proxy, though.

ADD COMMENTlink written 7 months ago by h.mon29k
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