TBProfiler

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Question about source of tbdb.spoligotype_list.csv

1

I was wondering what the source of the reference file for spoligotyping "tbdb.spoligotype_list.csv" is and how it is generated? It seems to be from SITVIT2 given the lineage column with...

RikkeMLarsen

Enabling strict WHO database mode

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Hi @jodyphelan, We were thinking that it would be good to have an option that ensures that only the WHO catalogue gets used for resistance calling. Is this something that...

vrennie

tb-profiler update_tbdb

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taobilin@VirtualBox:~$ tb-profiler update_tbdb Running command: set -u pipefail; git pull Running command: set -u pipefail; tb-profiler create_db Traceback (most recent call last): File "/home/taobilin/.local/bin/tb-profiler", line 693, in args.func(args) File "/home/taobilin/.local/bin/tb-profiler",...

BjoerlingTaul

lineage - how it works?

1

I have a question regarding how tbprofiler assigns lineages. I understand that lineages are determined by identifying lineage-specific SNPs. However, I am not familiar with the specific details or algorithm...

alantsangmb

tb_profiler docker version 5.0.1; update_tbdb produces "No such file or directory: 'variables.json'" Error

2

Running this image: staphb/tbprofiler latest 128a49b25724 which is the latest version 5.0.1 (base) root@5cdf3e69e18c:/home/robertbaldwin/tb_test/TB/calc_depth_bowtie_M.tb# tb-profiler update_tbdb --match_ref /home/robertbaldwin/tb_test/TB/calc_depth_bowtie_M.tb/sequence.fasta [08:59:17] ERROR Traceback (most recent call last): utils.py:391 File "/opt/conda/bin/tb-profiler", line 562,...

robertwhbaldwin

Exception: Don't know how to handle this mutation

1

Thanks for the great tool. This looks similar to https://github.com/jodyphelan/TBProfiler/issues/258 but on official latest ([1656b7fe64c5543d55cf52b55de67b2344e9564f](https://github.com/jodyphelan/tbdb/tree/1656b7fe64c5543d55cf52b55de67b2344e9564f)) tbdb. It may just be that you haven't had a chance to update tb-profiler yet...

schorlton

Hi Jody, I read in https://jodyphelan.github.io/TBProfiler/en/lineages/ that the lineages are assigned according to the papers from Coll et al., and further refined with the results from Napier et al. and...

BenjaminLokk

Hi Jody, I am interested in using the phylogenetic tools you had added to version 5. I quite dont understand how to use the functionality. If I run: tb-profiler profile...

jeffreybm

Bedaquiline resistance sequence

1

Hello There, I want to get the bedaquiline resistance gene sequences. Unfortunately the sequences are not present in any of the AMR database. I found mutations but I am not...

pratibha-kadam

Fazri

1

"his run has failed. Please check all arguments and make sure all input files exist. If no solution is found, please open up an issue at https://github.com/jodyphelan/TBProfiler/issues/new and paste or...

fazrisam