Alternatives and similar repositories for aquascope

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

• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆38Updated 2 months ago
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆26Updated 3 weeks ago
• DOH-JDJ0303 / vaper
  Viral (meta)-genome assembly pipeline.
  ☆17Updated last week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 3 months ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated 2 years ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated 3 months ago
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆40Updated 2 weeks ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 3 weeks ago
• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆15Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 4 months ago
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated this week
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆32Updated last month
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆18Updated last year
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆70Updated 2 years ago
• noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
  Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
  ☆21Updated last month
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆27Updated 2 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆29Updated last month
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆60Updated 2 weeks ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆61Updated 2 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆97Updated 3 months ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 6 months ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• nf-core / createtaxdb
  Parallelised and automated construction of metagenomic classifier databases of different tools
  ☆20Updated 2 weeks ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆24Updated 3 months ago
• quevan / phlame
  ☆12Updated 4 months ago