Julien A Nguinkal comments

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Julien A Nguinkal

RA failed - unequal lengths in sequence and overlap file for sequence with id xxxxx

Hi Robert, As expected (and feared) ra has failed because of RAM overload :( I think, our data load and computational resources are just not suitable to run ra in...

RA failed - unequal lengths in sequence and overlap file for sequence with id xxxxx

But according to your workflow description in github, even, with only TGS data, racon is ran twice over the preliminary PB only-based assembly. By manual polishing, you probably mean, polishing...

Chromap Bed output are not compatible with SALSA2 input bed format ?

SALSA2 expects a sorted (by reads name) bed file like this one: ``` ContigID Start End ReadName/ID XXX Strand ONT_Shasta_78 818203 818283 A00126:181:HMKLJDSX2:1:1101:10945:1000/1 60 + ONT_Shasta_78 817912 817984 A00126:181:HMKLJDSX2:1:1101:10945:1000/1 60...

Weird k-mers histogram : How to filter out /exclude k-mers under a depth threshold with hifiasm

Yes @chhylp123 , hifiasm produced contigs but with a few issues making the assembly suboptimal: - The assembly size is much larger (~200 Mb) than the estimated genome size (1200...

Weird k-mers histogram : How to filter out /exclude k-mers under a depth threshold with hifiasm

I think excluding low coverage k-mers (depth

Weird k-mers histogram : How to filter out /exclude k-mers under a depth threshold with hifiasm

Is the coverage information of contigs recorded in one of the hifiasm output files? Otherwise, I'll need to map HiFi-reads to the assembly to infer the contigs coverage.