Question: Assembly size decreased after using SSPACE for scaffolding
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gravatar for deepti1rao
5 months ago by
deepti1rao30
deepti1rao30 wrote:

I had 57,206 contigs from the Velvet assembler, with an N50 of 15,957. I got an assembly size of 348,942,280 bp (without any Ns).

When I fed these contigs into SSPACE, the N50 improved to 30,443, but my assembly size decreased to 348,541,909 bp, despite the inclusion of 31,358 Ns.

I used the same paired-end data for scaffolding with SSPACE, that I had initially used to build the contigs with Velvet.

How did the size of my assembly reduce?

ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 5 months ago by deepti1rao30

I never used SSPACE, but there's a few options. First would be to drop very short contigs. Second would be to merge sequences that the initial assembler kept seperate. However, I'd be suspious when scaffolding with the same input data yields so much better N50. Do you fancy to try other assemblers?

ADD REPLYlink written 5 months ago by Carambakaracho2.2k
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