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!
1 answer
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.
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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
I'll try to contact them, thank you.