Question: Does Minia discard singletons?
0
gravatar for stacy734
2.7 years ago by
stacy73440
stacy73440 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 • 649 views
ADD COMMENTlink modified 2.1 years ago by Rayan Chikhi1.4k • written 2.7 years ago by stacy73440
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gravatar for Rayan Chikhi
2.1 years 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 2.1 years ago • written 2.1 years ago by Rayan Chikhi1.4k
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