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
  ☆164Updated 3 months ago
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆125Updated this week
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆80Updated last year
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆140Updated 2 weeks 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
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆200Updated this week
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆153Updated 4 months ago
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆125Updated this week
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆99Updated 4 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• rrwick / Perfect-bacterial-genome-tutorial
  ☆144Updated last year
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆149Updated last month
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆174Updated 2 weeks ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆91Updated 3 weeks ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆141Updated last month
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆135Updated 5 months ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆104Updated 6 months ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆111Updated last year
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 3 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆125Updated last week
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated 2 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆140Updated last year
• 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…
  ☆146Updated 4 months ago
• treangenlab / emu
  ☆59Updated last month
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆82Updated 4 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• qiyunlab / HGTector
  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
  ☆136Updated last year
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆141Updated last year
• rrwick / Metagenomics-Index-Correction
  ☆84Updated last year