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singlem Public
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
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smafa Public
Biological sequence aligner for pre-aligned sequences
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fasttree Public
Forked from morgannprice/fasttreeFastTree 2: Approximately-Maximum-Likelihood Trees for Large Alignments
C GNU General Public License v3.0 UpdatedApr 30, 2026 -
GeneRax Public
Forked from BenoitMorel/GeneRaxC++ GNU Affero General Public License v3.0 UpdatedApr 26, 2026 -
GeneRaxCore Public
Forked from BenoitMorel/GeneRaxCoreCode used in both GeneRax and AleRax
C++ UpdatedApr 26, 2026 -
bbbin Public
A collection of working and non-working bioinformatics scripts
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sandpiper Public
Website / continuous DB builds for SingleM
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kingfisher-download Public
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
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CoverM Public
Read alignment statistics for metagenomics
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OrfM Public
simple and not slow ORF caller
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell UpdatedMar 25, 2026 -
orfm-rs Public archive
Pure-Rust port of OrfM - a simple and not slow open reading frame (ORF) caller
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hmmer-rs Public
Ergonomic Rust interface to HMMER
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Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene…
C++ UpdatedMar 21, 2026 -
is_it_paired Public
Check if a FASTA/FASTQ file appears to contain paired reads
Rust BSD 3-Clause "New" or "Revised" License UpdatedMar 20, 2026 -
sylph Public
Forked from bluenote-1577/sylphultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Rust MIT License UpdatedMar 20, 2026 -
singlem-sra-processing Public
Internal pipelines for singlem+sandpiper
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galah Public
More scalable dereplication for metagenome assembled genomes
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aviary Public
Forked from rhysnewell/aviaryA snakemake pipeline for binning metagenomic assemblies
Python BSD 3-Clause "New" or "Revised" License UpdatedMar 2, 2026 -
microbiome-ml Public
Forked from thepatientwait/microbiome-mlModule for microbiome based machine learning.
Python UpdatedMar 2, 2026 -
labubu-fraction-game Public
Labubu Fraction Quest - educational fractions & decimals game for 6th graders
HTML UpdatedFeb 26, 2026 -
rosella Public
Forked from rhysnewell/rosellaMetagenomic Binning Algorithm
Rust BSD 3-Clause "New" or "Revised" License UpdatedJan 16, 2026 -
hpc_scripts Public
Forked from centre-for-microbiome-research/hpc_scriptsScripts for easier use of the QUT HPC system
Python UpdatedJan 10, 2026 -
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floria Public
Forked from bluenote-1577/floriaStrain-level haplotyping for metagenomes with short or long-reads.
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singlem-installation Public
Containerised testing of SingleM installation methods
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nanomotif Public
Forked from MicrobialDarkMatter/nanomotifNanomotif - a tool for identifying methylated motifs in metagenomic samples
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