Documentation for analyzing SARS-Cov2 samples.
☆12Jun 4, 2020Updated 5 years ago
Alternatives and similar repositories for SARS-Cov2_analysis
Users that are interested in SARS-Cov2_analysis are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical bi…☆18Sep 1, 2023Updated 2 years ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 3 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 6 months ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22May 9, 2026Updated last week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- ☆10Feb 28, 2018Updated 8 years ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- SARS-CoV-2 genomics☆16Jun 20, 2025Updated 11 months ago
- Scripts, utilities and programs for genomic bioinformatics.☆83May 12, 2026Updated last week
- Identify Variants of Concern from metagenomic samples of SARS-CoV-2☆13Sep 9, 2021Updated 4 years ago
- Assembly and intrahost / low-frequency variant calling for viral samples☆15Feb 12, 2020Updated 6 years ago
- Fast sequence distance estimates☆28May 13, 2026Updated last week
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- Script for parsing SAM/BAM files for coverage statistics☆16Jun 13, 2023Updated 2 years 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.
- Intra-species bacterial contamination detection☆25Apr 13, 2026Updated last month
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- SARS-CoV-2 workflow for nanopore sequence data☆42Apr 15, 2026Updated last month
- Variant call verification☆17May 12, 2025Updated last year
- A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, Lo…☆20Jul 11, 2024Updated last year
- ☆23Apr 13, 2026Updated last month
- The CRISPR assembler☆35May 13, 2021Updated 5 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆39Apr 6, 2026Updated last month
- A pipeline for Bacterial Whole genome sequence data analysis☆15Jul 24, 2022Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated 10 months ago
- Genomic Assemblies Merger for NGS☆26Nov 10, 2023Updated 2 years ago
- Public Health England SNP calling pipeline.☆37Sep 4, 2018Updated 7 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
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20May 11, 2026Updated last week
- FLASH (Fast Length Adjustment of SHort reads); mirror of https://git.code.sf.net/p/flashpage/code☆13Mar 6, 2018Updated 8 years ago
- Real-time species-typing visualisation for nanopore data.☆13Apr 11, 2023Updated 3 years ago
- SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data☆20Jan 24, 2022Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Dec 11, 2020Updated 5 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree☆36Updated this week
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 5 years ago