cov-lineages / pangolin-dataLinks
Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
☆32Updated last month
Alternatives and similar repositories for pangolin-data
Users that are interested in pangolin-data are comparing it to the libraries listed below
Sorting:
- ☆50Updated 3 years ago
 - Depth-weighted De-Mixing☆123Updated last week
 - Consensus sequences for U.S. H5N1 clade 2.3.4.4b☆36Updated this week
 - Cluster Investigation & Virus Epidemiology Tool☆50Updated 4 months ago
 - Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Updated last year
 - Reconstruction of transmission trees using genomic data☆63Updated 2 years ago
 - Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆57Updated 2 years ago
 - Bayesian inference of ancestral dates on bacterial phylogenetic trees☆92Updated 2 months ago
 - A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated last year
 - ☆36Updated 6 months ago
 - Influenza data pipeline to automate genotyping assignment☆37Updated 2 weeks ago
 - Phylogenetics between and within hosts at once, all along the genome.☆50Updated last year
 - TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated 2 weeks ago
 - Programmatically interact with the GISAID database.☆78Updated 2 months ago
 - Reference-based consensus creation☆57Updated this week
 - PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated 2 months ago
 - Primer schemes for real-time genome epidemiology☆30Updated 2 years ago
 - Bioinformatics Pipeline and Visualization resources☆59Updated last year
 - 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Updated 2 years ago
 - Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆50Updated 3 years ago
 - Utility to alias and dealias pango lineages☆23Updated last year
 - SC2 variant detection and composition pipeline☆17Updated 2 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…☆36Updated 3 years ago
 - treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆104Updated 8 months ago
 - GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆83Updated 10 months ago
 - Ultrafast Sample Placement on Existing Trees☆134Updated this week
 - Split Kmer Analysis☆65Updated 3 years ago
 - INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆38Updated 3 weeks ago
 - Bifrost graph gene caller.☆95Updated last month
 - Rapid analysis and visualization of coronavirus genome variation☆48Updated last month