CNIDARIA: fast, reference-free phylogenomic clustering
Manual & Wiki: https://github.com/sauloal/cnidaria/wiki
Cnidaria does not need to be compiled but if you really want to, please refer to INSTALL.md.
Motivation: Identification of biological specimens is a major requirement
for a range of applications. Reference-free methods analyse unprocessed
sequencing data without relying on prior knowledge, but these do not scale
to arbitrarily large genomes and arbitrarily large phylogenetic distances.
Results: We present Cnidaria, a practical tool for clustering genomic and
transcriptomic data with no limitation on ge-nome size or phylogenetic
distances. We successfully simultaneously clustered 169 genomic and
transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at
supra-species level and 78% accuracy for species level.
Availability and Implementation: Cnidaria is written in C++ and Python and
is available at http://www.ab.wur.nl/cnidaria