Question: Does Minia discard singletons?
0
gravatar for stacy734
9 months ago by
stacy73420
stacy73420 wrote:

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

minia • 257 views
ADD COMMENTlink modified 12 weeks ago by Rayan Chikhi1.2k • written 9 months ago by stacy73420
0
gravatar for Rayan Chikhi
12 weeks ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

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.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Rayan Chikhi1.2k
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