Alternatives and similar repositories for skani:

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

• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆68Updated last year
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆153Updated 8 months ago
• wwood / singlem
  Novelty-inclusive microbial community profiling of shotgun metagenomes
  ☆138Updated last week
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆115Updated 2 weeks ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆115Updated last year
• rpetit3 / dragonflye
  Assemble bacterial isolate genomes from Nanopore reads
  ☆121Updated 3 weeks ago
• rhysnewell / aviary
  A hybrid assembly and MAG recovery pipeline (and more!)
  ☆87Updated this week
• GaetanBenoitDev / metaMDBG
  MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
  ☆133Updated 2 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆109Updated this week
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆112Updated 8 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆101Updated 3 years ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆107Updated last year
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆159Updated 9 months ago
• biobakery / phylophlan
  Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
  ☆133Updated last month
• cmks / DAS_Tool
  DAS Tool
  ☆146Updated 9 months ago
• ncbi / SKESA
  SKESA assembler
  ☆114Updated 4 months ago
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆208Updated last month
• gbouras13 / pharokka
  fast phage annotation program
  ☆153Updated 3 weeks ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆97Updated 3 weeks ago
• robotoD / GenoVi
  GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
  ☆86Updated last year
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆81Updated last year
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆75Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆74Updated this week
• phac-nml / staramr
  Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
  ☆131Updated last month
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆92Updated 2 years ago
• AnantharamanLab / ViWrap
  A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
  ☆70Updated last month
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆111Updated last year
• MaestSi / MetONTIIME
  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
  ☆91Updated 8 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆73Updated 5 months ago
• chklovski / CheckM2
  Assessing the quality of metagenome-derived genome bins using machine learning
  ☆195Updated last week