epi2me-labs / wf-metagenomicsView external linksLinks
Metagenomic classification of long-read sequencing data
☆101Jan 22, 2026Updated 3 weeks ago
Alternatives and similar repositories for wf-metagenomics
Users that are interested in wf-metagenomics are comparing it to the libraries listed below
Sorting:
- ☆44Jan 23, 2026Updated 3 weeks ago
- Small variant calling for haploid samples☆48Jan 5, 2026Updated last month
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆86Feb 5, 2026Updated last week
- ☆26Aug 2, 2023Updated 2 years ago
- TAXnomic Profile Aggregation and STAndardisation☆41Nov 18, 2025Updated 2 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 6, 2026Updated last week
- ☆48Dec 15, 2025Updated 2 months ago
- A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework☆117Jan 8, 2026Updated last month
- Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics☆199Feb 2, 2026Updated 2 weeks ago
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆199Feb 2, 2026Updated 2 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 9 months ago
- Graph-based assembly phasing☆91Nov 25, 2025Updated 2 months ago
- ☆82Jan 16, 2026Updated last month
- ☆79Updated this week
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆178Updated this week
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated 3 weeks ago
- Pipeline for the identification of (coding) gene structures in draft genomes.☆36May 9, 2024Updated last year
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- ☆232Feb 3, 2026Updated 2 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Jul 18, 2025Updated 6 months ago
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- A Nextflow pipeline for genome and pan-genome annotation☆15Feb 3, 2026Updated 2 weeks ago
- map Illumina metagenomes to genomes!☆38Jan 22, 2026Updated 3 weeks ago
- Ultra-fast preprocessing and quality control for long-read sequencing data☆219Sep 6, 2025Updated 5 months ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆114Nov 20, 2023Updated 2 years ago
- ☆41Dec 15, 2025Updated 2 months ago
- A post sequencing QC tool for Oxford Nanopore sequencers☆106Updated this week
- Materials for the STAMPS 2024 course at the MBL in Woods Hole, MA, USA☆13Jul 25, 2024Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆18Dec 12, 2025Updated 2 months ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated last year
- a long read simulator that can imitate many types of read problems☆267Jul 22, 2024Updated last year
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- Comparison of multiple long read datasets☆157Dec 2, 2025Updated 2 months ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆36May 14, 2025Updated 9 months ago
- A repository for collecting GPU basecalling stats☆76Feb 10, 2026Updated last week
- Bioinformatics program inStrain☆181May 9, 2025Updated 9 months ago
- Automated strain separation of low-complexity metagenomes☆52Nov 10, 2021Updated 4 years ago