smaller contigs

[yang yu]

Hi,

I installed metabat v 2.12.1. When I use metabat2, I want to binning contigs with contigs<1000bp, but I found that the minimum contigs length is 1500. Then I found the noAdd parameter, but I don’t know how to set it? Looking forward to hearing from you, thank you!

[yang yu]

sorry,it is “I want to binning contigs with contigs>1000bp“！I made a mistake。

[yang yu]

This is my code:

metabat2 -t 24 -i /home/iozac/huangy1/yuyang/metaspades/$base/scaffolds.fasta -m 1000 --noAdd -a /home/iozac/huangy1/yuyang/metabat/${base}.depth.txt -o /home/iozac/huangy1/yuyang/metabat/bin/${base}/$base

It will still report errors“Contig length < 1500 is not allowed to be used for binning.”

[Rob Egan]

Hi Yang Yu,

The 1500 contig length setting is hard coded and is there for a very good reason.

The desire to bin shorter contigs is understandable and shared, but below that threshold we have found that significantly more errors are introduced into the results, and therefore have set the default at the higher threshold of 2500 bases.

The information inferred from the TNF similarity and the abundance similarity are greatly affected by the contig lengths and therefore we have tuned MetaBAT to the information levels available above 1500 bases. Since there is no setting to disable it you would have to modify the source code and we could not stand behind results from that modification as they have proven unacceptable to us during development.

Using the --noAdd option will have the opposite effect you desire as it will not add contigs between 1500 and 2500 bases into your bins. Without the --noAdd option, after the bins have been reliably established at the 2500 base level, smaller contigs are considered to be added to the already established bins.

[yang yu]

thank you very much!