Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
☆15Feb 27, 2024Updated 2 years ago
Alternatives and similar repositories for ampseer
Users that are interested in ampseer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10May 15, 2026Updated last week
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆60Mar 23, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Repo for PrimerSchemes☆17May 15, 2026Updated last week
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 5 months ago
- Rust bindings for the tskit library☆18May 13, 2026Updated last week
- A novel method for sequence similarity estimation☆28Mar 23, 2024Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 3 years ago
- emm Automatic Isolate Labeller☆13Mar 25, 2025Updated last year
- A tool to detect acquired AMR genes directly from long read sequencing data.☆28Jan 31, 2026Updated 3 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆19Mar 25, 2026Updated 2 months ago
- Colinear block visualisation tool☆31Jan 17, 2024Updated 2 years ago
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆56Updated this week
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 6 months ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆16Apr 22, 2026Updated last month
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- Genome size estimation from long read overlaps☆89May 1, 2026Updated 3 weeks ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆62Updated this week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13May 5, 2026Updated 2 weeks ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Jul 16, 2024Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated 3 months ago
- ☆30Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- 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 4 years ago
- Fasten toolkit, for streaming operations on fastq files☆82Oct 24, 2025Updated 7 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated 10 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆11Jan 6, 2023Updated 3 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 2 weeks ago
- ☆20May 11, 2026Updated 2 weeks ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- ☆25Jun 25, 2024Updated last year
- Code Safety Inspection Service☆20Sep 23, 2022Updated 3 years ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49May 14, 2026Updated last week