Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
☆49Feb 26, 2026Updated last week
Alternatives and similar repositories for EsViritu
Users that are interested in EsViritu are comparing it to the libraries listed below
Sorting:
- Discover and annotate the virome☆59Feb 11, 2026Updated 3 weeks ago
- Opinionated viral metagenomics workflow☆11Feb 23, 2026Updated last week
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆23Nov 24, 2025Updated 3 months ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆37Aug 4, 2024Updated last year
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆38Jan 22, 2026Updated last month
- ☆21Updated this week
- Computation of average nucleotide identity with the use of MMseqs2☆15Dec 11, 2024Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆87Dec 27, 2024Updated last year
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)☆55Jan 19, 2024Updated 2 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.☆18Aug 16, 2021Updated 4 years ago
- BinaRena: Interactive Visualization and Binning of Metagenomic Contigs☆33Aug 22, 2024Updated last year
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years ago
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆78Apr 16, 2025Updated 10 months ago
- VirBot: a protein-based RNA virus detector for metagenomic data☆34Jul 29, 2024Updated last year
- 🦠🧬 Unraveling Viral Genomes from Metagenomes☆10Oct 3, 2025Updated 5 months ago
- vaginal microbiota☆12Jan 21, 2025Updated last year
- ☆15May 22, 2025Updated 9 months ago
- Integrative virome pipeline☆13Nov 4, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- Code for de novo discovery of viral families in virome data☆16Jun 20, 2024Updated last year
- A Hierarchical Approach to Pangenomics Inference☆13Apr 15, 2024Updated last year
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)☆22May 3, 2025Updated 10 months ago
- Reconstruction and analysis of viral and host genomes at multi-organ level☆21Jul 3, 2025Updated 8 months ago
- VirID: An integrated platform for the discovery and characterization of RNA Viruses☆23Jan 8, 2026Updated last month
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆147Updated this week
- ☆38Dec 6, 2023Updated 2 years ago
- This is a deep learning method for identification of viral contigs with short length from metagenomic data.☆10Dec 20, 2021Updated 4 years ago
- Parallelised and automated construction of metagenomic classifier databases of different tools☆20Feb 20, 2026Updated 2 weeks ago
- Supporting code for uncultivated gut virus manuscript☆77Jul 17, 2023Updated 2 years ago
- Taxonomic classification of viruses at Order and Family level☆21Mar 1, 2023Updated 3 years ago
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆166Jan 2, 2026Updated 2 months ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 2 months ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 8 months ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆69Sep 26, 2024Updated last year