nextstrain / nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
☆222Updated last month
Alternatives and similar repositories for nextclade:
Users that are interested in nextclade are comparing it to the libraries listed below
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆282Updated this week
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆168Updated last year
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆233Updated 2 weeks ago
- Assembly and intrahost/low-frequency variant calling for viral samples☆129Updated 2 weeks ago
- An updated pipeline for pangenome investigation☆274Updated 3 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆216Updated last year
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆126Updated last month
- NCBI Prokaryotic Genome Annotation Pipeline☆325Updated last week
- A user-friendly workflow for phylogenomics☆204Updated last week
- Processing pipeline for pan-genome visulization and exploration☆137Updated last year
- Viral genomics analysis pipelines☆191Updated 4 months ago
- Pan-genome wide association studies☆173Updated 7 months ago
- A tool to circularize genome assemblies☆233Updated 9 months ago
- Read alignment statistics for metagenomics☆314Updated last week
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆261Updated last month
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆343Updated last month
- pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…☆273Updated 3 months ago
- breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inte…☆154Updated 2 weeks ago
- Rapid comparison and dereplication of genomes☆272Updated last month
- Bacterial ribosomal RNA predictor☆231Updated last year
- NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org☆261Updated last week
- A flexible pipeline for complete analysis of bacterial genomes☆427Updated last month
- Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics☆181Updated last month
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆181Updated 5 months ago
- Scan contig files against PubMLST typing schemes☆206Updated 2 years ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆315Updated 2 weeks ago
- HyPhy: Hypothesis testing using Phylogenies☆225Updated 2 weeks ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆132Updated last month
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆180Updated last week
- customizable pipeline to identify viral sequences from (meta)genomic data☆234Updated last month