cov-lineages / pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
☆431Updated 3 months ago
Alternatives and similar repositories for pangolin:
Users that are interested in pangolin are comparing it to the libraries listed below
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆222Updated last month
- Store of the trained model for pangolin to access.☆55Updated 2 years ago
- A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.☆348Updated last year
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆282Updated this week
- Official repository for the QIIME 2 framework.☆483Updated this week
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆168Updated last year
- Automatically exported from code.google.com/p/figtree☆403Updated 9 months ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆343Updated last month
- PhyML -- Phylogenetic estimation using (Maximum) Likelihood☆180Updated 3 weeks ago
- hybrid assembly pipeline for bacterial genomes☆578Updated 5 months ago
- Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the…☆240Updated 7 months ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆233Updated 2 weeks ago
- Interactively explore metagenomes and more from a web browser.☆467Updated 3 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆427Updated last month
- Depth-weighted De-Mixing☆107Updated this week
- 🌈 Interactive analysis of metagenomics data☆408Updated 4 months ago
- Accurate sample inference from amplicon data with single nucleotide resolution☆484Updated 2 weeks ago
- The second version of the Kraken taxonomic sequence classification system☆748Updated this week
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆319Updated this week
- bioBakery tools for meta'omic profiling☆265Updated 3 months ago
- Ultra-deep search for novel viruses☆263Updated last year
- A grammar of graphics for comparative genomics☆636Updated last month
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆181Updated 5 months ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆495Updated last month
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆216Updated last year
- Mass screening of contigs for antimicrobial and virulence genes☆382Updated last year
- Gene cluster comparison figure generator☆551Updated last month
- NCBI Prokaryotic Genome Annotation Pipeline☆325Updated last week
- Code, unit tests, and tutorials for running PICRUSt2☆332Updated last week
- Read alignment statistics for metagenomics☆314Updated last week