skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
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Updated
Apr 20, 2024 - Python
skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
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
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
Approximate nearest neighbour search for microbial genomes based on hash metric
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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