VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
☆23Oct 21, 2025Updated 10 months ago
Alternatives and similar repositories for VILOCA
Users that are interested in VILOCA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆19Nov 24, 2025Updated 9 months ago
- Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)☆42Feb 24, 2023Updated 3 years ago
- ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and H…☆10May 3, 2018Updated 8 years ago
- Map single-cell transcriptomes to copy number evolutionary trees.☆14Aug 18, 2024Updated 2 years ago
- ☆30Mar 6, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- V-pipe is a pipeline designed for analysing NGS data of short viral genomes☆149Aug 2, 2026Updated last month
- Front-end code for Serratus project website☆11Jul 2, 2024Updated 2 years ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆24Feb 22, 2026Updated 6 months ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- Inference in Bayesian Networks with R☆12Feb 6, 2023Updated 3 years ago
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆21Jul 3, 2026Updated 2 months ago
- ☆27Dec 2, 2022Updated 3 years ago
- ☆13Jul 21, 2025Updated last year
- Quality control for phylogenetic analyses☆13Updated this week
- 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.
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- ☆32Sep 21, 2023Updated 2 years ago
- Python library for identification and masking of low-complexity regions in nucleotide sequences☆14Aug 10, 2026Updated 3 weeks ago
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 8 years ago
- ☆14Feb 9, 2026Updated 6 months ago
- ☆23Jul 22, 2026Updated last month
- Single-cell Iso Prep☆17Oct 28, 2023Updated 2 years ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆55Mar 23, 2026Updated 5 months ago
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆48Aug 5, 2026Updated 3 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆111Jul 7, 2026Updated last month
- ☆48Oct 2, 2023Updated 2 years ago
- Data Structures for Bioinformatics - LM Bioinformatics - University of Rome Tor Vergata☆12Feb 27, 2026Updated 6 months ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- Deep exponential families for single-cell data.☆21Aug 17, 2026Updated 2 weeks ago
- Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification☆15Sep 27, 2023Updated 2 years ago
- SARS-CoV-2 workflow for nanopore sequence data☆42Aug 13, 2026Updated 3 weeks ago
- Repo for PrimerSchemes☆20Jul 6, 2026Updated last month
- The viral taxonomic assignment pipeline☆46Updated this week
- 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.
- A set of Pyro models and functions to infer CNA from scRNA-seq data☆11Aug 14, 2023Updated 3 years ago
- a tool for designing primer panels for multiplex PCR.☆111Feb 5, 2024Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆137Updated this week
- Simple Manipulation Of Trees☆14Aug 16, 2025Updated last year
- Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.☆14Dec 4, 2025Updated 8 months ago
- LoFreq Star: Sensitive variant calling from sequencing data☆112Oct 16, 2025Updated 10 months ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆42Apr 6, 2026Updated 4 months ago