Alternatives and similar repositories for vadr

Users that are interested in vadr are comparing it to the libraries listed below

• sanger-pathogens / ariba
  Antimicrobial Resistance Identification By Assembly
  ☆181Updated 2 years ago
• W-L / ProblematicSites_SARS-CoV2
  ☆50Updated 3 years ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆59Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆101Updated 3 years ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆58Updated 7 months ago
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 5 months ago
• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated last year
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆142Updated last year
• ncbi / SKESA
  SKESA assembler
  ☆123Updated last year
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 2 months ago
• ddarriba / modeltest
  Best-fit model selection
  ☆85Updated last year
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆88Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• maximilianh / multiSub
  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
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆75Updated last year
• lskatz / mashtree
  Create a tree using Mash distances
  ☆172Updated 2 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 6 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆116Updated last year
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated 11 months ago
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆57Updated 2 years ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆144Updated last week
• chanzuckerberg / czid-workflows
  Portable WDL workflows for CZ ID production pipelines
  ☆47Updated 4 months ago
• sanger-pathogens / pathogen-informatics-training
  ☆75Updated 4 years ago
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆56Updated this week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆120Updated last month
• arpcard / amr_curation
  A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…
  ☆63Updated last month
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆103Updated 7 months ago
• artic-network / fieldbioinformatics
  The ARTIC fieldbioinformatics pipeline
  ☆125Updated 2 weeks ago
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆30Updated 2 years ago
• artic-network / rampart
  Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
  ☆82Updated 7 months ago