How to reduce Quast stats being based on "contigs of size

How to reduce Quast stats being based on "contigs of size > 100000 bp"

1

Entering edit mode

4.3 years ago

kristina.mahan ▴ 170

I am using conda installed Quast v5.0.2 to generate stats for genome assemblies. The report indicates "All statistics are based on contigs of size >= 100000 bp . . ." How can I change this so that the stats are based on contigs >= 1000 bp?

quast • 1.3k views

ADD COMMENT • link updated 14 months ago by Ram 44k • written 4.3 years ago by kristina.mahan ▴ 170

0

Entering edit mode

potentially not the answer you're expecting but did you check the manual (or help) of Quast?

100Kb sounds rather large as default btw.

ADD REPLY • link 4.3 years ago by lieven.sterck 15k

0

Entering edit mode

yes definitely. It says you can specify contig length but default is 500. I am not specifying contig length and the report says that the stats are based on contigs >= 100,000. So I am not sure what is happening.

ADD REPLY • link 4.3 years ago by kristina.mahan ▴ 170

0

Entering edit mode

ok, that's something already.

can you post the exact command line you are executing?

ADD REPLY • link 4.3 years ago by lieven.sterck 15k

Login before adding your answer.