Surveillance of pathogens using population genomics and sequencing
☆62Oct 27, 2026Updated last week
Alternatives and similar repositories for pathogensurveillance
Users that are interested in pathogensurveillance are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- A Python package for working with Bactopia☆12Aug 5, 2026Updated 2 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Oct 27, 2026Updated last week
- Ultra-rapid detection of viral variants directly from sequencing data☆49Sep 16, 2026Updated last month
- ☆20Sep 16, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Parallelised and automated construction of metagenomic classifier databases of different tools☆22Oct 27, 2026Updated last week
- Influenza genome analysis Nextflow workflow☆28Jun 3, 2026Updated 5 months ago
- ☆16Jan 21, 2024Updated 2 years ago
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆193Updated this week
- Quickly generate consensus assemblies for bacterial genomes☆14Sep 12, 2025Updated last year
- Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets☆25Apr 30, 2026Updated 6 months ago
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆113Sep 30, 2026Updated last month
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆36Oct 6, 2026Updated 3 weeks ago
- ☆26Jul 25, 2026Updated 3 months ago
- 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.
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆42Updated this week
- Nextflow version of SNVPhyl☆12Oct 24, 2024Updated 2 years ago
- ☆22Oct 20, 2026Updated 2 weeks ago
- VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact…☆16Jul 21, 2026Updated 3 months ago
- Compare the quality of multiple genomes, along with their annotations.☆26Oct 26, 2026Updated last week
- A toolbox for pangenome analysis and threshold evaluation.☆103Jul 8, 2022Updated 4 years ago
- Genome browser 🧬👀🚀☆35Aug 24, 2026Updated 2 months ago
- Taxonomic Reconstruction and Analysis of NGS Amplicons - A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads…☆24Oct 27, 2026Updated last week
- ☆39Updated this week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆84Updated this week
- A tool to aid virus sequencing and accelerate IRMA.☆13Updated this week
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆182Aug 10, 2026Updated 2 months ago
- Searching large collections of sequencing data with genome-scale queries☆23Oct 25, 2026Updated last week
- Workflow for MAG quality assessment and taxonomical annotation.☆15May 26, 2026Updated 5 months ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆15Oct 9, 2026Updated 3 weeks ago
- k-mers and the like☆22Oct 18, 2026Updated 2 weeks ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆209Jun 10, 2026Updated 4 months ago
- Split k-mer analysis – version 2☆109Oct 20, 2026Updated 2 weeks ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.☆15Oct 19, 2026Updated 2 weeks ago
- A Nextflow pipeline for running synteny analysis.☆20Aug 2, 2026Updated 3 months ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆58Jul 24, 2025Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆15Jun 5, 2026Updated 4 months ago
- Metagenomic classification of long-read sequencing data☆112Jan 22, 2026Updated 9 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆67Jun 16, 2025Updated last year
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆97Jul 23, 2026Updated 3 months ago