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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Minimum contig length in metaSPAdes #410

Closed Marcoleta-AE closed 4 years ago

Marcoleta-AE commented 4 years ago

Thanks for this awesome tool. I successfully used it to assemble soil metagenomes using illumina and nanopore reads. However, I could not find what is the minimum size of the assembled contigs (set as default, could it be set to a defined value by the user?). After running QUAST with my assemblies, I can see only # contigs (>= 0 bp) and then (>1000 bp), so I cannot figure out the size of those contigs under 1 kbp.

Thanks for your help!

Best Regards

asl commented 4 years ago

Hello

Thank you for your interest in SPAdes.

There is no minimum contig length. Certainly, the contig could not be shorter than the maximum used k-mer length.