Lior Glick comments

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                                            Lior Glick

Conda recipe

Any updates?

Why did it go to Chr0?

Thanks for the quick reply. Indeed this worked. I think this parameter should definitely be externalized.

Output contig locations bed file

Thanks. Can this script also extract mapping coordinates on the reference? If not, how can I extract them from the PAF? How should I treat cases of incomplete mapping and/or...

Output contig locations bed file

Is there a way to tell which alignments that informed scaffolding?

Output contig locations bed file

Thanks - I'll give it a try. Could be a nice addition to the output (as requested in my original post)

QUAST ignoring bam files

Thanks Alla. That worked indeed. Is there a scheduled date for the next release?

Feature request: allow downloading from GSA

Yes, there is indeed a problem of documentation there. I was only able to construct this command after consulting with the GSA support team. I should say that they were...

Different Run Times Contigs vs. Chromosomes

I am also experiencing very slow runs with chromosomes-to-chromosomes mapping. I see this is a rather old issue - are there any updates on that? I don't see memory/swapping problems...

How to generate multi-samples kmer count table?

Just wanted to say that I also find this useful and would be glad to see improvement and integration into kmc_tools. Thanks!

Correct mapping but strange gene model

Another relevant observation - TransDecoder seems to do a better job at predicting the CDS sequence, given the transcripts extracted from the GAWN output, so that might be a lead...