nextstrain / nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
☆227Updated this week
Alternatives and similar repositories for nextclade:
Users that are interested in nextclade are comparing it to the libraries listed below
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆221Updated 2 years ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆298Updated last month
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆268Updated this week
- Pan-genome wide association studies☆191Updated 10 months ago
- Assembly and intrahost/low-frequency variant calling for viral samples☆133Updated this week
- Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data☆114Updated last week
- Scan contig files against PubMLST typing schemes☆220Updated 2 years ago
- Rapid comparison and dereplication of genomes☆280Updated 3 months ago
- Bacterial ribosomal RNA predictor☆238Updated last year
- customizable pipeline to identify viral sequences from (meta)genomic data☆243Updated 4 months ago
- A flexible pipeline for complete analysis of bacterial genomes☆449Updated last week
- NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org☆275Updated last week
- Viral genomics analysis pipelines☆192Updated 6 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆317Updated 10 months ago
- Read alignment statistics for metagenomics☆324Updated this week
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Updated 2 years ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆356Updated this week
- Build a partitioned pangenome graph from microbial genomes☆262Updated this week
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆136Updated 3 months ago
- An updated pipeline for pangenome investigation☆290Updated 3 weeks ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆238Updated last week
- A tool to circularize genome assemblies☆239Updated 11 months ago
- SEER, reimplemented in python 🐍🔮☆120Updated 5 months ago
- A user-friendly workflow for phylogenomics☆209Updated this week
- Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics☆185Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆142Updated 3 months ago
- Fast genome analysis from unassembled short reads☆284Updated 11 months ago
- Assemble bacterial isolate genomes from Nanopore reads☆123Updated 2 months ago
- Synteny and Rearrangement Identifier☆371Updated this week
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆107Updated last year