Romain Derelle

this isn't an issue, rather a strange observation. I have mapped a set of genes on a genome assembly of the same species (but another lineage) using the option -ax...

error: alignment contains sequences of unequal length

8

Hi, I have generated an alignment between 2 genomes using progressiveMauve (default parameters) and I'm now trying to extract SNPs using snp-sites. My issue is that I get the error...

install failed with python 3.7 on MacOS (SSLCertVerificationError)

5

I am trying to install parasail on my computer but it does not seem to work. I am using python 3.7 on Mac OS. with the following command: >> python3...

potential issue with lineage typing

1

Dear Jody, I came across some strange results for a SRA sample (ERR4797559) which is supposed to be part of the lineage 1.2.2 according to the tb-profiler website and confirmed...

Feature requests: different mixture model; combined ska build & cov

2

Hi John, Thanks a lot for implementing the calculation of the optimal kmer count threshold (ska cov). I tested it using ska 0.3.1 and a paired-end sample (fastq files available...

Ideally, an automatic detection of the coverage threshold (min-count parameter) could be used when building skf files. This would allow for the analyse of any set of fastq files, regardless...

suggestion: new input option for ska build (1 file containing n isolates)

2

I’ve been playing a bit with SKA2 and a dataset of around 2400 mpox genomes to test k-mer sizes and SNP callers. It worked well overall, but I found it...