Depth-weighted De-Mixing
☆127Mar 1, 2026Updated this week
Alternatives and similar repositories for Freyja
Users that are interested in Freyja are comparing it to the libraries listed below
Sorting:
- SC2 variant detection and composition pipeline☆19Jul 14, 2023Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆134Updated this week
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- ☆19Nov 24, 2025Updated 3 months ago
- SARS-CoV-2 (Va)riant (Qu)antification in s(E)wage, designed for (Ro)bustness☆13Oct 10, 2025Updated 4 months ago
- Datasets for https://github.com/nextstrain/nextclade☆44Updated this week
- Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification☆15Sep 27, 2023Updated 2 years ago
- SARS-Cov-2 Recombinant Finder for fasta sequences☆50Jun 22, 2022Updated 3 years ago
- UPHL's Reference Free Pipeline☆27Updated this week
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Feb 19, 2026Updated last week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Updated this week
- ☆22Feb 2, 2026Updated last month
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated 3 weeks ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆16Nov 24, 2025Updated 3 months ago
- Nextstrain build for avian influenza viruses☆27Feb 13, 2026Updated 2 weeks ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Apr 25, 2024Updated last year
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated last month
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆251Updated this week
- Assembly and intrahost/low-frequency variant calling for viral samples☆157Feb 23, 2026Updated last week
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆23Sep 30, 2025Updated 5 months ago
- ☆74Jan 23, 2024Updated 2 years ago
- ☆21Feb 12, 2026Updated 2 weeks ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- ☆12Feb 15, 2023Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- Software for the Tree-Based Scan Statistic☆14Feb 23, 2026Updated last week
- Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments☆32Feb 17, 2026Updated last week
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 2 years ago
- SARS-CoV-2 genomics☆16Jun 20, 2025Updated 8 months ago
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆60Mar 23, 2023Updated 2 years ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 3 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- ☆10Apr 16, 2025Updated 10 months ago
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Mar 22, 2023Updated 2 years ago
- snipit: summarise snps relative to your reference sequence☆167Jan 13, 2026Updated last month
- ☆30Mar 6, 2025Updated 11 months ago