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nanometa_live Public
Forked from FOI-Bioinformatics/nanometa_liveA streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline …
Python GNU General Public License v3.0 UpdatedMar 16, 2026 -
bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
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TRANA Public
Forked from genomic-medicine-sweden/TRANAA pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
Nextflow GNU General Public License v3.0 UpdatedDec 12, 2025 -
StringMeUp Public
Forked from danisven/StringMeUpA post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.
Python MIT License UpdatedNov 4, 2025 -
taxprofiler Public
Forked from nf-core/taxprofilerHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Nextflow MIT License UpdatedOct 24, 2025 -
metapresence Public
Forked from MetabioinfomicsLab/metapresenceMetapresence is a Python tool to calculate metrics to assess the evenness of the coverage distribution on DNA sequences, in order to infer their presence in a given sample.
Python UpdatedOct 9, 2025 -
YACHT Public
Forked from KoslickiLab/YACHTA mathematically characterized hypothesis test for organism presence/absence in a metagenome
C++ MIT License UpdatedSep 14, 2025 -
flextaxd Public
Forked from FOI-Bioinformatics/flextaxdFlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Python GNU General Public License v3.0 UpdatedSep 9, 2025 -
reportHanter Public
An interactive HTML report generator for sequence classification analyses.
Python MIT License UpdatedAug 22, 2025 -
taxpasta Public
Forked from taxprofiler/taxpastaTAXnomic Profile Aggregation and STAndardisation
Python Apache License 2.0 UpdatedAug 19, 2025 -
vocabulator Public
vocabulator is a small application to train languages
Python MIT License UpdatedAug 2, 2025 -
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SourceID-NMF Public
Forked from ZiyiHuang0708/SourceID-NMFMicrobial source tracking via Non-negative Matrix Factorization
Python UpdatedApr 3, 2025 -
PolyTrap Public
PolyTrap: A flexible Snakemake pipeline for designing optimized capture probes targeting multiple organisms with customizable priority levels
Python GNU General Public License v3.0 UpdatedApr 3, 2025 -
PuumaProbes Public
A streamlined Snakemake pipeline for designing highly specific probes targeting Puumala virus segments, with enhanced focus on segment flanks to ensure comprehensive coverage.
Python MIT License UpdatedJan 22, 2025 -
preprimer Public
Forked from FOI-Bioinformatics/preprimerPrepare primers from different formats, i.e. schemes for tiled sequencing from varvamp to artic format. Also prepares and aligns primers with mepcr or exonerate.
Python GNU General Public License v3.0 UpdatedDec 10, 2024 -
misc_scripts Public
Miscellaneous useful scripts (genomics related)
Python GNU General Public License v3.0 UpdatedDec 8, 2024 -
sdsl-lite-feedstock Public
Forked from conda-forge/sdsl-lite-feedstockA conda-smithy repository for sdsl-lite.
Shell BSD 3-Clause "New" or "Revised" License UpdatedSep 4, 2024 -
conda-forge-pinning-feedstock Public
Forked from conda-forge/conda-forge-pinning-feedstockA conda-smithy repository for conda-forge-pinning.
Python BSD 3-Clause "New" or "Revised" License UpdatedSep 3, 2024 -
argutils-feedstock Public
Forked from conda-forge/argutils-feedstockA conda-smithy repository for argutils.
BSD 3-Clause "New" or "Revised" License UpdatedJun 12, 2024 -
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TreeToReads Public
Forked from snacktavish/TreeToReadsPipeline to generate NGS reads from a phylogeny
Python Other UpdatedApr 3, 2024 -
krakenhll Public
Forked from fbreitwieser/krakenuniqKrakenHLL metagenomics classification method with unique k-mer counting for more specific results
C++ GNU General Public License v3.0 UpdatedApr 3, 2024 -
amptk Public
Forked from nextgenusfs/amptkAMPtk: Amplicon ToolKit for NGS data (formally UFITS)
Python BSD 2-Clause "Simplified" License UpdatedApr 3, 2024 -
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 UpdatedMar 21, 2024 -
Lilo Public
Forked from amandawarr/LiloStitch together Nanopore tiled amplicon data without polishing a reference
Python UpdatedNov 29, 2023 -
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