average-nucleotide-identity

There are 17 repositories under average-nucleotide-identity topic.

  • widdowquinn/pyani

    Application and Python module for average nucleotide identity analyses of microbes.

    Language:Python1921125355

  • bluenote-1577/skani

    Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

    Language:Rust16352810

  • bluenote-1577/sylph

    ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

    Language:Rust1363146

  • refresh-bio/vclust

    Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

    Language:Python44391

  • jean-pierreBoth/gsearch

    Approximate nearest neighbour search for microbial genomes based on hash metric

    Language:Rust39437

  • raufs/skDER

    skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

    Language:Python39153

  • althonos/pyskani

    PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

    Language:Rust20201

  • althonos/pyfastani

    Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

    Language:Cython18301

  • althonos/orthoani

    A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.

    Language:Python17422

  • lmc297/BTyper3

    In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

    Language:Python17460

  • lmc297/bactaxR

    Bacterial taxonomy construction and evaluation in R

    Language:R12364

  • YoukaiFromAccounting/skandiver

    skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)

    Language:Python8100

  • lmc297/BTyper

    Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

    6311

  • sophiagosselin/tANI_tool

    Script for creating a tANI distance matrix for use in phylogenetic reconstruction.

    Language:Perl1152

  • wu-lab-uva/FastANI-Rebuttal

    R Code to reproduce results in the Nature Communication paper: Murray, C.S., Gao, Y. & Wu, M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nat Commun 12, 4059 (2021). https://doi.org/10.1038/s41467-021-24128-2

    Language:R1200

  • lucaTriboli/DiMHepy

    Python module that provide an alternative view of the outputs produced by the software pyani

    Language:Python0010

  • refresh-bio/LZ-ANI

    Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes

    Language:C++