The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format
☆14Apr 21, 2023Updated 3 years ago
Alternatives and similar repositories for sars2variantcalling
Users that are interested in sars2variantcalling are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated 2 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 2 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆16Feb 19, 2026Updated 6 months ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆19Updated this week
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Apr 1, 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.
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆14Jan 6, 2023Updated 3 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 9 months ago
- Our laboratory repository☆11Jan 12, 2021Updated 5 years ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 2 months ago
- Documentation for NCBI BLAST AMI☆11Feb 28, 2022Updated 4 years ago
- Multiplex PCR design, in silico☆24Mar 4, 2025Updated last year
- VIGOR4☆23Aug 15, 2025Updated last year
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years 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.
- finding conserved regions in highly diverse genomes☆16May 25, 2026Updated 3 months ago
- Kraken2 Server☆23Nov 24, 2025Updated 9 months ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆14May 23, 2023Updated 3 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆57Jul 24, 2025Updated last year
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated last year
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.☆20Feb 26, 2026Updated 6 months 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.
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Dec 14, 2022Updated 3 years ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆15Jun 14, 2022Updated 4 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Catalog of genomic indexes freely available from public clouds☆75Jul 27, 2026Updated last month
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆18Oct 5, 2019Updated 6 years ago
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated last month
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- ☆23Apr 2, 2026Updated 4 months ago
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆76Aug 13, 2026Updated 2 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jul 17, 2026Updated last month
- Influenza genome analysis Nextflow workflow☆27Jun 3, 2026Updated 2 months ago
- 🦠🧬 Unraveling Viral Genomes from Metagenomes☆11Jul 30, 2026Updated last month
- Ultra fast FASTQ and BAM processing, filtering, concatenation and sequencing QC/statistics.☆58Mar 4, 2026Updated 5 months ago
- ☆27Aug 2, 2023Updated 3 years ago
- Python toolbox for multi-omics data mapping and analysis☆29Apr 13, 2023Updated 3 years ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago