search

Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
25 stars 8 forks source link

Resistome #26

Open GKerdivel opened 1 year ago

GKerdivel commented 1 year ago

Hi,

I was testing the pipeline on some of my own data and I obtained no results (without errors) despite the fact that I know that there is some resistance genes in these data and looking at the bam I could see some mapping on the appropriate genes. However I wanted to check where the things could be wrong and realize that I could not debug anything as the problem seems to lie within the resistome binary. Thus my questions are : 1) What exactly are the steps performed within this resistome binary? 2) Could it be possible to share the source code?

Thanks a lot for your work and your fast answers !

PS : I re-downloaded the singularity image yesterday evening and still had the problem with the snp module observed by someone else

stalbrec commented 9 months ago

Hi,

i'd also like to know more about the version of the resistome binary. As far as i can tell from the source code used in the previous AMR++ versions (cdeanj/resistomeanalyzer), there have been made some changes. Any pointers/info would be greatly appriciated. :)