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sequana
sequana

Sequana: a set of Snakemake NGS pipelines

6K 151 27
althonos
pyfastani

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

5K 24 2
Imageomics
pybioclip

Python package and CLI that simplifies using the BioCLIP family of foundation models.

4K 61 13
Changwanseo
funvip

Fungal Validation and Identification Pipeline

4K 14 0
althonos
pyskani

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

3K 29 2
PnX-SI
taxhub

Application web de gestion centralisée des taxons basée sur le référentiel TAXREF

3K 26 38
antonheitz
xbrl-forge

Generate XBRL Instances, iXBRL instances, xBRL Taxonomies and xBRL extension taxonomies from distributed sources

3K 6 2
Ecogenomics
gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

3K 593 97
lverweijen
littletree

Tree data structure

3K 4 0
widdowquinn
pyani

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

3K 216 56
saezlab
omnipath-client

Python client for the new OmniPath web APIs

2K 0 0
pirovc
multitax

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

1K 50 4
saezlab
omnipath-utils

Prior-knowledge processing utilities Python package, database and web API

1K 0 0
Changwanseo
genmine

GenBank Record downloader for taxonomists

981 8 0
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

953 39 15
profjsb
tdtax

Open, versioned taxonomy for astronomical time-series sources

849 12 9
SweBiTS
joltax

JolTax is a high-performance, vectorized taxonomy library for Python.

703 0 0
CVUA-RRW
taxidtools

A Python Toolkit for Taxonomy

635 3 2
moshi4
aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

523 92 12
gem
openquake-gem-taxonomy-data

Openquake Gem Building Taxonomy Data - GEM building taxonomy data and python classes to access it.

517 1 0
pyinat
naturtag

Tag your nature photos with iNat taxonomy and observation metadata

490 52 3
linzhi2013
taxonomy-ranks

To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)

487 9 4
ggonnella
fastsubtrees

Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

447 4 0
smdabdoub
kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

433 60 16
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