A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
☆19Jan 8, 2026Updated 2 months ago
Alternatives and similar repositories for MAGMA
Users that are interested in MAGMA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- A snakemake workflow for WGS-based tuberculosis transmission analysis☆19Dec 3, 2024Updated last year
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆47Sep 8, 2025Updated 6 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- Mycobacterium tuberculosis next generation sequence analysis☆24Oct 11, 2019Updated 6 years ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆13Jul 28, 2025Updated 7 months ago
- Extract subsets of ONT (Nanopore) reads based on time☆23Sep 12, 2024Updated last year
- ☆14Jun 30, 2021Updated 4 years ago
- µbinfie blog☆19Jul 21, 2025Updated 8 months ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated last year
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Influenza genome analysis Nextflow workflow☆31Sep 15, 2025Updated 6 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- Organism-specific interpretation of AMR genotypes☆15Mar 17, 2026Updated last week
- A simple pipeline for bacterial assembly and quality control☆16Updated this week
- Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data☆133Updated this week
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 3 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- ☆30Updated this week
- ☆21Jan 23, 2026Updated 2 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆54Oct 24, 2025Updated 5 months ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Reference-based consensus creation☆60Mar 17, 2026Updated last week
- resources for bioinformatics education☆102May 14, 2025Updated 10 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- ☆10Apr 16, 2025Updated 11 months ago
- Converts bam or cram files to fastq format and does quality control.☆32Jan 22, 2026Updated 2 months ago
- ☆17Dec 4, 2025Updated 3 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆15Aug 5, 2022Updated 3 years ago