Vadim A. Pisarenco

Hello! I just downloaded the latest version of MaSuRCA-4.0.8 and tried to run samba pipeline using PacBio CLR reads as input. Here is my script: ```bash #!/bin/bash -x #$ -cwd...

Hello @ruanjue ! We have to assemble a genome with the following features: - Genome size: ~2Gb - High repetitiveness: ~78.68% (inferred from a close species) - Hi AT content:...

wtpoa-cns polishing details

9

Good morning! I would like to ask if you can provide a more explicit explanation about what "wtpoa-cns" does. I've been looking around in literature and internet and a I've...

Hello! We've tried to run broccoli with different ratio_ortho values: 0.5 (default), 0.3 and 0.7. It turned out that the results were IDENTICAL for all the values. Is this expected?...

Good morning! I tried to run your software. Everything seems to be ok. However I found that there are some proteins (few cases) that have been assigned twice, to different...

Advice. Use only chromosomes as reference or the entire assembly?

1

Hi! I'm trying to us ntJoin to scaffold an input PacBio CLR genome assembly using a chromosome level assembly of a closely related species as a refence. 1) I would...

Multithreading issue with ~3000 protein files (10seq per file). Any advice?

1

Hi! We would like to run Broccoli on a huge dataset of 3000 with ~10 seq in each one. Have you tried something as this? How the multithreading could be...

Neutral mutation rate argument error

1

Hi! I'm trying to run EDTA using a custom Neutral mutation rate value, "4.07e-9". But I'm getting the following error: `Argument "4.07eM-bM-^HM-^R9" isn't numeric in multiplication (*) at /myuser/anaconda3/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line...