☆16Jun 30, 2021Updated 5 years ago
Alternatives and similar repositories for fast-lineage-caller
Users that are interested in fast-lineage-caller 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☆15Jun 5, 2026Updated 5 months ago
- A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research☆20Updated this week
- Profiling NTM WGS data☆19Oct 24, 2026Updated 2 weeks ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆48Sep 8, 2025Updated last year
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆14Feb 9, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A snakemake workflow for WGS-based tuberculosis transmission analysis☆20Dec 3, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Oct 27, 2026Updated last week
- Read contamination removal☆24Jan 24, 2024Updated 2 years ago
- An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.☆14Updated this week
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- Mycobacterial pipeline☆11Sep 11, 2025Updated last year
- Simulate mutations in genomes☆15Jun 15, 2020Updated 6 years ago
- In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies☆10Aug 6, 2024Updated 2 years ago
- Wide and Deep Neural Net for predicting TB resistance from genotypic data☆15Dec 9, 2019Updated 6 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Drug Resistance Prediction with Reference Graphs☆21Oct 23, 2025Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data☆14Oct 25, 2026Updated last week
- Mycobacterium tuberculosis complex lineage typing☆11Jun 22, 2025Updated last year
- Pipeline for creating comprehensive viral reference sets.☆12Oct 28, 2026Updated last week
- Assembly topology from long-read alignments☆10Jul 24, 2026Updated 3 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆31Jul 18, 2025Updated last year
- Uses cDBG to count unitigs in bacterial populations☆20Feb 15, 2023Updated 3 years ago
- A deletion finder through re-aligning the whole soft-clipping read☆12Jul 2, 2016Updated 10 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data☆143Oct 25, 2026Updated last week
- In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)☆10Jun 17, 2026Updated 4 months ago
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 7 years ago
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated 3 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 27, 2026Updated 3 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Welcome to the StrainHub Repo - Files and Data - StrainHub Online:☆20Jun 26, 2022Updated 4 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆27Sep 12, 2024Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- exploring viral genome assembly with variation graph tools☆20May 18, 2020Updated 6 years ago
- Add biological annotations to variants in a given VCF file.☆33Apr 4, 2026Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 4 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated 2 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆115Oct 12, 2026Updated 3 weeks ago
- Customer workshop materials☆19May 13, 2026Updated 5 months ago
- Workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.☆11Oct 7, 2026Updated last month