PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
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Updated
Apr 11, 2023 - Rust
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
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
Python module that provide an alternative view of the outputs produced by the software pyani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data
skDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
Script for creating a tANI distance matrix for use in phylogenetic reconstruction.
Bacterial taxonomy construction and evaluation in R
Approximate nearest neighbour search for microbial genomes based on hash metric
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Application and Python module for average nucleotide identity analyses of microbes.
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