GitHub topics: average-nucleotide-identity
althonos/pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
Language: Cython - Size: 430 KB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 23 - Forks: 2
pyani-plus/pyani-plus
Development repo for pyani-plus (the next iteration of pyani)
Language: Python - Size: 12.8 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 16 - Forks: 2
refresh-bio/vclust
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
Language: Python - Size: 10.6 MB - Last synced at: 11 days ago - Pushed at: 4 months ago - Stars: 88 - Forks: 4
althonos/pyskani
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
Language: Rust - Size: 2.87 MB - Last synced at: 6 days ago - Pushed at: 17 days ago - Stars: 27 - Forks: 2
raufs/skDER
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
Language: Python - Size: 164 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 49 - Forks: 4
bluenote-1577/skani
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Language: Rust - Size: 72.9 MB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 210 - Forks: 13
bluenote-1577/sylph
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Language: Rust - Size: 27.6 MB - Last synced at: 24 days ago - Pushed at: 2 months ago - Stars: 239 - Forks: 9
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: Python - Size: 380 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 0
jean-pierreBoth/gsearch
Approximate nearest neighbour search for microbial genomes based on hash metric
Language: Rust - Size: 39.1 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 56 - Forks: 8
lmc297/BTyper3
In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data
Language: Python - Size: 6.48 MB - Last synced at: 21 days ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 0
althonos/pyorthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
Language: Python - Size: 2.23 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 31 - Forks: 4
widdowquinn/pyani 📦
Application and Python module for average nucleotide identity analyses of microbes.
Language: Python - Size: 185 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 215 - Forks: 57
refresh-bio/LZ-ANI
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
Language: C++ - Size: 1.25 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0
sophiagosselin/tANI_tool
Script for creating a tANI distance matrix for use in phylogenetic reconstruction.
Language: Perl - Size: 142 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 2
lmc297/BTyper
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
Size: 24.7 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 1
lmc297/bactaxR
Bacterial taxonomy construction and evaluation in R
Language: R - Size: 601 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 3
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: R - Size: 11 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
lucaTriboli/DiMHepy
Python module that provide an alternative view of the outputs produced by the software pyani
Language: Python - Size: 431 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
