Alternatives and similar repositories for Freyja

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

• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆163Updated 2 months ago
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆122Updated this week
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆197Updated 3 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆152Updated 3 months ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 5 months ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆131Updated 2 months ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆153Updated last week
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆148Updated 3 weeks ago
• rrwick / Perfect-bacterial-genome-tutorial
  ☆137Updated last year
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆79Updated 10 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆121Updated 3 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆96Updated 3 months ago
• arpcard / amr_curation
  A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…
  ☆59Updated 7 months ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆76Updated 2 years 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
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆233Updated 2 weeks ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆58Updated this week
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆125Updated last month
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆72Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆67Updated 2 months ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated last month
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆145Updated 2 months ago
• Saskia-Oosterbroek / decona
  fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
  ☆49Updated 11 months ago
• bede / hostile
  Precise host read removal
  ☆102Updated last month
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• gbouras13 / pharokka
  fast phage annotation program
  ☆168Updated 3 weeks ago
• pha4ge / hAMRonization
  Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
  ☆160Updated last month
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated 2 months ago