Vadim A. Pisarenco

Great news! By the way, will you update the bioconda version of Augustus as well? This would be great since I'm trying to install Augustus locally in a computer cluster...

Hello! But, in principle, should the RNA-seq mapping with STAR be performed on either unmasked/softmaked genome as suggested here #241 ? Shouldn't it? By the way, we run into the...

> You should always visually inspect structural genome annotation in a Genome Browser in context with evidence. Vadim A. Pisarenco ***@***.***> schrieb am Mo. 27. Juni 2022 um 12:26: Understood,...

Hello! We followed this steps (wtdbg2 protocol from the main github page) to assembly and polish our genome: 1) ~57x PacBio reads cov (genome size ~ 1.5 Gb) were assembled...

Good morning! Many thanks, it was very helpful! I forgot to mention that our genome is highly repetitive (~60%). I have checked what you have asked for: indels size. For...

Good morning! Many thanks for the suggestions! Here are the Merqury and BUSCO results. - Merqury values don't achieve 30 threshold but at least **PB+IL qv** is higher than **PB...

Good morning! At the beginning of this issues, you have mentioned this "it implemented an adaptive-banded SIMD POA". I looked for it and found a description (abbreviated as abPOA) [here](https://academic.oup.com/bioinformatics/article/37/15/2209/5962085)....

Hi @lcoombe ! Thanks for clear and detailed explanation. Both species have a divergence of ~5 Mya and the BUSCO scores are quite similar when comparing `nocut=True` vs `nocut=False`, although...