Aeiou
Aeiou
Hi! I am trying a GWAS tutorial (https://pyseer.readthedocs.io/en/master/tutorial.html) which starts by using mash on multiple fasta files which correspond to assemblies. This tutorial has downloadable content which contains a single...
Dear all, I am running snippy core on a lot of samples (around 1000) but for processing reasons I cannot run snippy and then snippy-core on all samples at once....
Dear all, I came across an issue that seems to be common but I can't solve using previously suggested answers. My problem is as described in the title, I initially...
Hi! I have a big question. When running snippy-core are the low quality SNPs called with snippy filtered out? I'm running snippy+snippy-core on 386 E. coli isolates and I'm getting...
Dear @tseemann, I'm running an SNP phylogeny as you suggested here: https://github.com/tseemann/snippy My problem is that if I compare the nwk tree generated by gubbins and that from IQ-tree I...
Hi! I have a question regarding how to treat the snippy-core results to feed them into IQTree afterwards. So right now, I have the core.full.aln file, should I first go...
Hi! Sorry if this is a rather silly question but I've been reading and couldn't find an answer on this one. I've been using Kraken2-Bracken on metagenomes and it runs...
Hey Jennifer! First of all, thanks for the tool and the support you provide to users. I have a question regarding how things are calculated in Bracken. I understand that...
Hi everyone! I've run pavian both from R or directly from the webpage (which in the end is the same), the output is great with the added interactivity, I would...
Hi everyone! I'm trying to run args_oap using a custom database (PlasmidFinder). I downloaded the db and indexed the .fasta file using: `args_oap make_db -i ~/path/to/db/plasmid_db.fasta` Now I'm trying to...