CDCgov / datasets-sars-cov-2Links
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
☆54Updated 2 years ago
Alternatives and similar repositories for datasets-sars-cov-2
Users that are interested in datasets-sars-cov-2 are comparing it to the libraries listed below
Sorting:
- Bioinformatics Pipeline and Visualization resources☆55Updated 9 months ago
- Primer schemes for real-time genome epidemiology☆28Updated last year
- ARTIC SARS-CoV-2 workflow and reporting☆51Updated last month
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated 10 months ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆48Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated last month
- Harmonization of AMR predictor tool outputs☆25Updated 4 months ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated 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…☆35Updated 3 years ago
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆74Updated this week
- Benchmark datasets for WGS analysis☆39Updated 5 years ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆92Updated last year
- SC2 variant detection and composition pipeline☆17Updated last year
- SARS-CoV-2 workflow for nanopore sequence data☆40Updated 3 weeks ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆44Updated 9 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 11 months ago
- ☆49Updated 3 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆98Updated 2 months ago
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆31Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆52Updated this week
- This repository hosts a large collection of Nextflow snippets☆57Updated 4 months ago
- Standard database for the TBProfiler tool☆29Updated 2 months ago
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆94Updated last month
- Tutorial on using E-utilities☆22Updated 2 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…☆47Updated last year
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆27Updated this week
- de novo virus assembler of Illumina paired reads☆55Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆57Updated 2 months ago
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆48Updated 3 years ago