ivlachos / agamemnonView external linksLinks
Accurate metagenomi/metatranscriptomic analysis pipeline
☆23Jun 28, 2021Updated 4 years ago
Alternatives and similar repositories for agamemnon
Users that are interested in agamemnon are comparing it to the libraries listed below
Sorting:
- viralFlye pipeline☆18Aug 12, 2024Updated last year
- Pan-Genomic Matching Statistics☆55Apr 3, 2024Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.☆18Aug 16, 2021Updated 4 years ago
- ☆18Apr 6, 2022Updated 3 years ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆61Mar 25, 2024Updated last year
- ☆11Apr 5, 2021Updated 4 years ago
- Snakemake workflow to map and quantify microbial genomes in metagenomic reads☆13Oct 10, 2025Updated 4 months ago
- ☆22Nov 12, 2025Updated 3 months ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- exploring viral genome assembly with variation graph tools☆20May 18, 2020Updated 5 years ago
- genetic distance plotting for recombination events analysis☆10Nov 21, 2024Updated last year
- Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences☆10Sep 3, 2025Updated 5 months ago
- Integrative virome pipeline☆13Nov 4, 2024Updated last year
- Minimal Microbial Consortia creation tools☆13Jan 28, 2022Updated 4 years ago
- A Hierarchical Approach to Pangenomics Inference☆13Apr 15, 2024Updated last year
- Plot microbiome time series in parallel☆27Nov 7, 2023Updated 2 years ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆23Feb 5, 2025Updated last year
- ☆45Jun 27, 2023Updated 2 years ago
- ☆14Jan 31, 2026Updated 2 weeks ago
- Discover and annotate the virome☆58Updated this week
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture☆12Sep 22, 2022Updated 3 years ago
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated 7 months ago
- ViBE: a hierarchical BERT model to identify viruses using metagenome sequencing data☆11Sep 6, 2022Updated 3 years ago
- String algorithm visualizations☆13Feb 7, 2023Updated 3 years ago
- A metatranscriptomic pipeline optimized for the study of microeukaryotes.☆17Dec 30, 2025Updated last month
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- Improvement of metagenome-assembled genomes☆54Mar 17, 2020Updated 5 years ago
- Automatic eukaryotic taxonomic classification☆29May 9, 2025Updated 9 months ago
- Nanopore plasmid pipeline (FAST5 basecalling, assembly, plasmid identification and antimicrobial resistance genes identification).☆13Apr 20, 2021Updated 4 years ago
- Population genomics from metagenomes☆13Sep 1, 2024Updated last year
- Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.☆14Dec 4, 2025Updated 2 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated last year
- A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies☆32Jun 9, 2023Updated 2 years ago
- Metagenome analysis using the Kraken software suite☆36Sep 29, 2022Updated 3 years ago
- Bioinformatics program inStrain☆181May 9, 2025Updated 9 months ago