TB-ML-Containers

Welcome to the tb-ml-community page which serves as a centralised repository list of containers that can be used with tb-ml. Click on an individual container to find out more. For information on how to build containers and how to add them to this page, click on the contribute section.

Prediction containers

Name	Architecture	Drugs	Input	Docker
TB-AMR-CNN	CNN	amikacin, capreomycin, ciprofloxacin, ethambutol, ethionamide, isoniazid, kanamycin, levofloxacin, moxifloxacin, ofloxacin, pyrazinamide, rifampicin, streptomycin	One-hot-encoded-sequence/CSV	julibeg/tb-ml-neural-net-from-one-hot-encoded-seqs-13-drugs
tb-dr-pred-nn	CNN	amikacin, capreomycin, ciprofloxacin, ethambutol, ethionamide, isoniazid, kanamycin, levofloxacin, moxifloxacin, ofloxacin, pyrazinamide, rifampicin, streptomycin	One-hot-encoded-sequence/CSV	linfengwang/tb-dr-pred-nn
aggreen-MTB-CNN	CNN	amikacin, capreomycin, ciprofloxacin, ethambutol, ethionamide, isoniazid, kanamycin, levofloxacin, moxifloxacin, ofloxacin, pyrazinamide, rifampicin, streptomycin	consensus-sequences/FASTA	julibeg/tb-ml-aggreen-mtb-cnn
RF-Streptomycin	Random Forest	streptomycin	variants/CSV	julibeg/tb-ml-random-forest-from-variants-streptomycin
mykrobe	Direct Association	amikacin, capreomycin, ciprofloxacin, delamanid, ethambutol, ethionamide, isoniazid, kanamycin, levofloxacin, linezolid, moxifloxacin, ofloxacin, pyrazinamide, rifampicin, streptomycin	fastq	jodyphelan/mykrobe

Preprocessing containers

Name	Input	Features	Docker
raw2consensus	fastq	consensus-sequences/FASTA	julibeg/tb-ml-consensus-seqs-from-raw-reads
aln2variants	sam/bam/cram	variants	julibeg/tb-ml-variants-from-aligned-reads
raw2one-hot	fastq	One-hot-encoded-sequence/CSV	julibeg/tb-ml-one-hot-encoded-seqs-from-raw-reads
aln2one-hot	sam/bam	One-hot-encoded-sequence/CSV	julibeg/tb-ml-one-hot-encoded-seqs-from-aligned-reads