mycobacterium-tuberculosis

There are 0 repository under mycobacterium-tuberculosis topic.

jodyphelan / TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
drug-resistance mycobacterium tuberculosis ngs mycobacterium-tuberculosis
Language:Python 89
ngs-fzb / MTBseq_source
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
tuberculosis pipeline phylogeny variants epidemiology ngs genomics mycobacterium-tuberculosis
Language:Perl 38
farhat-lab / fast-lineage-caller
lineage-call mycobacterium-tuberculosis
Language:Python 12
mbhall88 / tbpore
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
mycobacterium-tuberculosis nanopore genomics bioinformatics variant-calling drug-resistance-prediction
Language:Python 11
TORCH-Consortium / MAGMA
A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
genomics pipeline mycobacterium-tuberculosis tuberculosis nextflow-pipeline nextflow
Language:Nextflow 11
mycobactopia-org / MTBseq-nf
MTBSeq made simple and easy using Nextflow and nf-core standard.
genomics mtb nextflow mycobacterium-tuberculosis
Language:Nextflow 8
dcouvin / SpolLineages
Rapid and precise prediction of Mycobacterium tuberculosis complex families
decision-tree mycobacterium-tuberculosis evolutionary-algorithm classification supervised-learning bioinformatics
Language:Java 6
HKU-BAL / ONT-TB-NF
Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.
bioinformatics bioinformatics-pipeline mycobacterium-tuberculosis nanopore nanopore-analysis-pipeline adaptive-sequencing
Language:Nextflow 5
dbespiatykh / RDscan
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
bioinformatics snakemake mycobacterium mycobacterium-tuberculosis-complex structural-variants bacterial-genome-analysis mycobacterium-tuberculosis
Language:Python 4
dmnfarrell / mtbdiff
Characterization of Mycobacterium tuberculosis complex species using mummer and nucdiff
genomics mycobacterium-tuberculosis microbiology bioinformatics
Language:Jupyter Notebook 4
BCCDC-PHL / tb-db
Database for storage of M. tuberculosis genomics analysis results
database microbial-genomics mycobacterium-tuberculosis
Language:Python 3
nf-core / tbanalyzer
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
mycobacterium-tuberculosis mycobacterium-tuberculosis-complex nextflow nf-core pipeline reproducible-research workflow
Language:Nextflow 3
safinaARK / MTB-VCF
Multipurpose tool for targeted variant calling of genetic polymorphisms in Mycobacterium Tuberculosis
drug-resistance mycobacterium-tuberculosis variant-calling
Language:C 3
a-r-j / TB-Resources
List of online databases and resources for Mycobacterium Tuberculosis
tuberculosis genomics integration curated list omics transcriptomics proteomics proteomics-datasets proteomics-data-integration proteomics-data transcriptomics-datasets transcriptomics-data-integration transcriptomics-data genomics-data genomics-data-sets mycobacterium mycobacterium-tuberculosis computational-biology drug-discovery
1
dbespiatykh / tblg
A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file
barcoding command-line genotyping mycobacterium-tuberculosis mycobacterium-tuberculosis-complex python
Language:Python 1
jananiravi / papers
comparative-genomics computational-biology host-pathogen molecular-evolution mycobacterium-tuberculosis phylogeny stress-response
1
nottwy / TB-DROP
Deep Learning-based A Tool used to Drug Resistance Prediction of Mycobacterium tuberculosis Utilizing Whole Genome Mutations
deep-learning drug-resistance-prediction mycobacterium-tuberculosis
Language:Python 1
dbespiatykh / TBvar
Variant detection and lineage barcoding of Mycobacterium tuberculosis
barcoding mycobacterium-tuberculosis snakemake variant-calling
Language:Python 0
MaryAgopian / Variant_Barcoding_M.orygis
Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.
bacterial bacterial-genome-analysis bacterial-genomes bioinformatics bioinformatics-pipeline genomic-data-analysis genomic-data-science genomics genomics-visualization microbial-genomes microbiology mycobacterium-bovis mycobacterium-tuberculosis mycobacterium-tuberculosis-complex tuberculosis mycobacterium-orygis
Language:R 0
PulmonomicsLab / mcdr-mtb-standalone
Multi-class classification of drug resistance in MTB clinical isolates
bwa-mem caret diagnostics drug-resistance-prediction freebayes machine-learning multi-class-classification mycobacterium-tuberculosis prediction r-programming samtools shell-script svm trimgalore variant-calling vcf whole-genome-sequencing
Language:Shell 0
rahimrajwani / Search-in-MTB-genomes
genomics-search mycobacterium-tuberculosis bioinformatics
Language:HTML 0
jananiravi / sigmafactor-network-mtb
2016 Sigma factor network in M. tuberculosis | https://jananiravi.github.io/publication/2016/natcomm/
mycobacterium-tuberculosis computational-biology sigma-factor network-biology
Language:R