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mycobacterium-tuberculosis-complex

Here are 11 public repositories matching this topic...

USDA-VS / vSNP

vSNP -- validate SNPs

bam-files snps pipeline genomics vcf phylogenetics snp wgs high-throughput-sequencing high tuberculosis whole-genome-sequencing analysis-pipeline mycobacterium-tuberculosis-complex brucella freebayes

Updated Nov 21, 2022
Python

dbespiatykh / RDscan

A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples

bioinformatics snakemake mycobacterium-tuberculosis-complex structural-variants mycobacterium-tuberculosis mycobacterium bacterial-genome-analysis

Updated Feb 9, 2024
Python

PathoGenOmics-Lab / mycolorsTB

R Color package for Mycobacterium tuberculosis complex

r-package mycobacterium-tuberculosis-complex colors-palette

Updated Apr 4, 2024
R

nf-core / tbanalyzer

An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.

workflow pipeline nextflow reproducible-research mycobacterium-tuberculosis-complex nf-core mycobacterium-tuberculosis

Updated May 9, 2024
Nextflow

USDA-VS / vSNP3

vSNP -- validate SNPs

bam-files snps pipeline genomics phylogenetics influenza wgs high-throughput-sequencing bwa-mem tuberculosis whole-genome-sequencing analysis-pipeline vcf-files mycobacterium-bovis mycobacterium-tuberculosis-complex mycobacterium-bovis-af2122 brucella freebayes sars-cov-2

Updated May 9, 2024
Python

dbespiatykh / tblg

A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

python command-line mycobacterium-tuberculosis-complex genotyping barcoding mycobacterium-tuberculosis

Updated Apr 6, 2023
Python

TB-gen

dbespiatykh / TB-gen

Web-app to explore Mycobacterium tuberculosis complex

tuberculosis mycobacterium-tuberculosis-complex barcoding streamlit streamlit-webapp

Updated Mar 23, 2024
Python

jananiravi / psp-mtb

Phage-shock-protein (psp) system in M. tuberculosis

evolution computational-biology psp mycobacterium-tuberculosis-complex stress-response

Updated Jan 16, 2019

rahimrajwani / MIRU-profiler

epidemiology tandem-repeats whole-genome-sequencing mycobacterium-tuberculosis-complex

Updated Jan 3, 2021
Shell

kerrimalone / M.bovis-AF2122-genome-update

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

pacbio genome-assembly illumina-sequencing de-novo-assembly reference-genome mycobacterium-bovis genome-update mycobacterium-tuberculosis-complex mycobacterium-bovis-af2122

Updated Jun 20, 2017
Shell

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.

bioinformatics genomics bioinformatics-pipeline microbiology microbial-genomes tuberculosis genomic-data-analysis genomics-visualization mycobacterium-bovis mycobacterium-tuberculosis-complex bacterial bacterial-genomes mycobacterium-tuberculosis genomic-data-science bacterial-genome-analysis mycobacterium-orygis

Updated Apr 26, 2022
R

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