Question: Does Minia discard singletons?
0
gravatar for stacy734
18 months ago by
stacy73430
stacy73430 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 • 433 views
ADD COMMENTlink modified 11 months ago by Rayan Chikhi1.4k • written 18 months ago by stacy73430
0
gravatar for Rayan Chikhi
11 months ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k 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 11 months ago • written 11 months ago by Rayan Chikhi1.4k
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