VStrains is a de novo approach for reconstructing strains from viral quasispecies.
☆24Updated this week
Alternatives and similar repositories for VStrains
Users that are interested in VStrains are comparing it to the libraries listed below
Sorting:
- ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs☆37Oct 24, 2025Updated 4 months ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆69Sep 26, 2024Updated last year
- ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes☆18Feb 3, 2026Updated 3 weeks ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆34May 23, 2025Updated 9 months ago
- Chimera: A Versatile Metagenomic Classification Tool☆20Feb 1, 2026Updated 3 weeks ago
- ☆13Dec 3, 2024Updated last year
- Haplotype-aware genome assembly toolkit☆30Jan 8, 2020Updated 6 years ago
- Set of tools for viral metagenomics.☆14Jan 21, 2026Updated last month
- Strain Resolution ON Graphs☆50Jul 18, 2023Updated 2 years ago
- Graph-based assembly phasing☆91Nov 25, 2025Updated 3 months ago
- Improvement of metagenome-assembled genomes☆54Mar 17, 2020Updated 5 years ago
- ☆20Sep 26, 2025Updated 5 months ago
- Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.☆14Dec 4, 2025Updated 2 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated this week
- exploring viral genome assembly with variation graph tools☆20May 18, 2020Updated 5 years ago
- Automated strain separation of low-complexity metagenomes☆52Nov 10, 2021Updated 4 years ago
- Pipeline to automatically analyse SARS-CoV-2 Whole genome sequencing Illumina data obtained using EasySeq SARS-CoV-2/COVID-19 Whole Geno…☆15Jul 26, 2022Updated 3 years ago
- Hierarchical binned indexed data store for on-disk genomic data.☆13Jan 18, 2025Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- ☆13Dec 26, 2025Updated 2 months ago
- ☆17Oct 7, 2024Updated last year
- ☆63Feb 27, 2024Updated 2 years ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆47Feb 12, 2026Updated 2 weeks ago
- Prefix-renaming FASTA records really fast.☆17Jun 26, 2024Updated last year
- Long-read aligner to pangenome graphs☆29May 20, 2024Updated last year
- VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data☆23Oct 21, 2025Updated 4 months ago
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆17Feb 3, 2026Updated 3 weeks ago
- Discover and annotate the virome☆59Feb 11, 2026Updated 2 weeks ago
- ☆30Sep 21, 2023Updated 2 years ago
- Supporting code for uncultivated gut virus manuscript☆77Jul 17, 2023Updated 2 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Apr 23, 2025Updated 10 months ago
- Pipeline for designing custom probes against human genes☆21Jan 30, 2026Updated last month
- ☆34Oct 6, 2025Updated 4 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆82Sep 8, 2025Updated 5 months ago
- Phasing of dikaryotic fungal genome assemblies☆13Mar 1, 2023Updated 2 years ago
- Methods to determine sequence element (unitig) presence/absence☆23Nov 24, 2025Updated 3 months ago