Colin Davenport

Hi, Abra is being picked up by a log4j vulnerability detection tool. I would guess the threat level is low (not web based), but am not sure. Is there any...

Hi, are there any plans to support single ended nanopore reads ? Thanks, Colin

Warning - contains an old (but likely not vulnerable?) version of log4J. java-genomics-toolkit/lib/BigWig.jar!/lib/log4j-1.2.15.jar contains Log4J-1.x

validator

7

Hi, thanks for this. I have a lot of problems with incorrect and weird samplesheets from the lab generated with "copy-paste" and strange barcode schemes, such as mixed Truseq and...

Phase retained?

1

Hi again, will the phase of the reads be retained following correction ? i.e. if I want to use the corrected reads for determining phasing and haplotypes , will this...

Error in docker docs ? Also perl error ?

2

Hi. Interesting approach, thanks ! Just trying the docker approach, I'm gettng the following issues. My system Ubuntu 1604, Perl 5.22 docker pull xiaolidong/docker-metaerg ### does not find the docker...

path

1

Hi everybody, I see in the requirements path.py is needed. I tried to install all of these, and downgraded cyvcf2 to version 0.2.8 I believe. A version for path.py is...

Pangenome presence absence viz ?

2

Dear devs, I'm interested in visualizing a pangenome matrix from odgi pavs in JBrowse1. Maybe someone has made something like this viewer, panache as an example. https://www.appliedbioinformatics.com.au/wheat_panache/ I think it...

Hi, I work on plants, which seem to be lacking with the precomputed MSAs available. What software would you recommend for creating genome scale MSAs of plants ? I can...

Quality log

3

Hi, maybe it would be possible to list the number of corrected bases per contig in an output log. This would be helpful for those with large genomes from novel...