Does Minia discard singletons?

Question

[stacy734]

Hi everyone,

I am working with some Minia assemblies. These were run using the no-length-cutoff parameter. Normally I discard small contigs, but I like to see what comes out before i do.

My question: when using the no-length-cutoff parameter, does Minia keep everything, even the singletons, reads which were not part of any contig?

Just curious.

Thanks for any information.

Stacy

Answer 1

[Rayan Chikhi]

Hi, yes Minia should keep singleton k-mers that were not filtered out by the abundance threshold. You can check this by looking at the length of the smallest contigs.