cov-lineages / lineages
Resources for calling and describing the circulating lineages of SARS-CoV-2
☆37Updated 3 years ago
Related projects: ⓘ
- FAST: Fast Analysis of Sequences Toolbox☆31Updated 4 years ago
- serious constellations of reoccurring phylogenetically-independent origin☆38Updated 11 months ago
- ☆14Updated 5 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆32Updated last week
- Classify sequencing reads using MinHash.☆47Updated 4 years ago
- SARS-CoV-2 variant calling and consensus assembly pipeline☆23Updated last year
- ☆8Updated 3 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 5 years ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆14Updated 6 months ago
- An integrated high performance bioinformatics toolkit☆23Updated 5 years ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Updated 5 years ago
- 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
- Cluster Investigation & Virus Epidemiology Tool☆48Updated last year
- Phylogenetics between and within hosts at once, all along the genome.☆44Updated last month
- Collection of utilities for working with PacBio-based assemblies☆13Updated last year
- Systematic ProtEin AnnotatoR☆19Updated this week
- Ebola virus surveillance☆16Updated 8 years ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆20Updated 7 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 5 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 3 years ago
- ☆19Updated 7 years ago
- ☆18Updated 8 years ago
- Get microbial sequence data easier and faster☆28Updated 4 years ago
- Public Health England SNP calling pipeline.☆36Updated 6 years ago
- Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree☆25Updated 6 years ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆23Updated last week
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆19Updated 8 years ago
- Validate and edit small eukaryotic genome assemblies☆31Updated last year
- Genomic Assemblies Merger for NGS☆26Updated 10 months ago
- ☆25Updated 3 years ago