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multitax Public
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
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metabench Public
MetaBench is a pipeline to run and benchmark metagenomics tools. It covers database construction, taxonomic binning and profiling.
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dudes Public
DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell UpdatedFeb 22, 2024 -
ganon Public
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hie…
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genome_updater Public
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
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grimer Public
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
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taxsbp Public
TaxSBP - Taxonomic structured bin packing implementation
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scikit-bio Public
Forked from scikit-bio/scikit-bioscikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
Python BSD 3-Clause "New" or "Revised" License UpdatedAug 25, 2021 -
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metameta Public
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pylca Public
Lowest common ancestor (LCA) algorithm implementation in Python
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staged-recipes Public
Forked from conda-forge/staged-recipesA place to submit conda recipes before they become fully fledged conda-forge feedstocks
Python BSD 3-Clause "New" or "Revised" License UpdatedApr 2, 2019 -
DecontamManuscript Public
Forked from benjjneb/DecontamManuscriptReprocible analyses accompanying the paper introducing the decontam method
HTML UpdatedNov 5, 2018 -
cxxopts Public
Forked from jarro2783/cxxoptsLightweight C++ command line option parser
C++ MIT License UpdatedMay 7, 2018 -
Frontiers_2017 Public
Forked from ggloor/Frontiers_2017Supplement for Frontiers article
TeX GNU General Public License v3.0 UpdatedApr 20, 2018 -
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ContamFilter Public
Forked from NCBI-Hackathons/ContamFilterImplements NCBI Contamination Screen Publicly in CWL
Python MIT License UpdatedNov 22, 2017 -
kmer_counting Public
Forked from algbioi/kmer_countingContains the source code for the new k-mer counting algorithm
C UpdatedSep 2, 2017 -
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binpacking Public
Forked from benmaier/binpackingAims at optimal distribution of weighted items to bins (either a fixed number of bins or a fixed number of volume per bin). Data may be in form of list, dictionary, list of tuples or csv-file.
Python MIT License UpdatedOct 26, 2016 -
lca-1 Public
Forked from saadtaame/lcaQuick lowest-common-ancestor queries using sparse tables.
C++ UpdatedMay 31, 2016 -
lca Public
Forked from mihai995/lcaA Comparison Between Various Lowest Common Ancestor Algorithms
C++ GNU General Public License v2.0 UpdatedMar 20, 2015 -
rmq Public
Forked from leifwalsh/rmqImplementations of LCA and RMQ data structures from "The LCA Problem Revisited"
C++ UpdatedAug 19, 2014 -