shlomobl

start with assembled genomes / cgMLST

1

Hi, 1) Is it possible to start the pipeline with assembled genomes? (if not, that would be a nice addition) 2) Can you add cgMLST to the analysis? (using PubMLST...

[bug] output in json format only

1

Hi, After updating to the last version of Bactopia, most output files are in json format. For example, BLAST, MLST, AMR... no txt files, only json. Any ideas what could...

[feature] Report

1

Hi, Is there already a way to wrap the results of different analysis into one report or file? Preferably csv, but also a html or similar report for visualization would...

Hi, It would be very nice if Bactopia could assign cgMLST typing from established cgMSLT schemes (PubMLST or else), either directly or by input of the scheme. Thanks!

Clustering

1

Hi, Can anyone suggest a tool to assign genomes to clusters based on fastANI matrix and a given cut-off? Thanks!

custom protein database

4

Hi, I am analyzing multiple bacterial genomes with very little programing knowledge. The way tormes parses and summarizes the results from all the genomes in tabular files is very helpful!...

Re-run with subset of samples

2

Hi, Is there a way to run part of the pipeline on a subset of the initial genomes, without running it all over again? For example, if there are some...

multiple sequence files

7

Dear all, I got 4 fastq files from seq provider (L1 to L4) instead of 2 as I was used to get with another provider. They told me is it...

Undo?

1

Hi, I just cannot find it - is there a "undo changes" option?