pha4ge / SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
☆34Updated 10 months ago
Related projects: ⓘ
- 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 2 years ago
- Bioinformatics Pipeline and Visualization resources☆53Updated 3 weeks ago
- Harmonization of AMR predictor tool outputs☆20Updated 10 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆32Updated last week
- ☆19Updated 2 months ago
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆54Updated last year
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆23Updated this week
- Nextstrain build for avian influenza viruses☆19Updated this week
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆25Updated 11 months ago
- Recombination-free trees☆55Updated last year
- Detection of incorrectly labeled sequences across kingdoms☆77Updated last year
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated last year
- Interpretative standards for AMR genotypes☆13Updated 2 months ago
- Phylogenetics between and within hosts at once, all along the genome.☆44Updated 3 weeks ago
- Utility to alias and dealias pango lineages☆21Updated 9 months ago
- Python Toolkit for using containerized programs in either Singularity or Docker☆25Updated 6 months ago
- SHallow shOtGUN profiler☆54Updated 2 years ago
- ☆22Updated 6 months ago
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆26Updated this week
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆48Updated 2 years ago
- Rapid determination of appropriate reference genomes.☆88Updated 8 months ago
- a collection of scripts for organising bacterial genomes by species☆75Updated 2 years ago
- de novo virus assembler of Illumina paired reads☆53Updated 3 years ago
- ASMNGS20 - 2020 Conference Details☆15Updated 2 years ago
- ☆43Updated 2 months ago
- Cluster Investigation & Virus Epidemiology Tool☆48Updated last year
- resources for bioinformatics education☆67Updated 6 months ago
- BEAV: Bacterial Element Annotation reVamped☆55Updated 2 weeks ago
- A tool for agile functional analysis of shotgun metagenomic data☆21Updated this week
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆27Updated 4 months ago