search

BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
Other
125 stars 48 forks source link

concoct on long reads and hybrid assemblies #279

Closed MChiaraC closed 5 years ago

MChiaraC commented 5 years ago

Hi, is there any chance concoct can work with assembly and coverage info coming from long reads only? Or short paired reads are the only ones working for this algorithm? In this second case should I bin hybrid assemblies using only short reads or is there still somehow a probability of bias?

Thanks!

alneberg commented 5 years ago

Hi @MChiaraC,

I think the coverage is the important thing here, if you have deep seequencing of long reads, it should work in theory (untested). But I guess the normal case is that you have quite low coverage from only long reads.

A hybrid assembly where the short reads are used for coverage estimation should work fine and sounds like a great idea if you have access to that kind of data. There's always probability of bias, don't dare to speculate in that...