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gtdbtk
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public |
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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2025-04-18 |
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annembed
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public |
annembed is an ultra-fast and scalable non-linear dimension reduction/embedding algorithm (similar to UMAP or t-SNE) for large-scale biological data
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2025-04-18 |
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msoma
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public |
mSOMA: Somatic Mutation Detection using a betabinomial null model
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2025-04-18 |
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mgnify-pipelines-toolkit
|
public |
Collection of scripts and tools for MGnify pipelines.
|
2025-04-18 |
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ucsc-cell-browser
|
public |
A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend.
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2025-04-18 |
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pybiolib
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public |
BioLib Python Client
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2025-04-18 |
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codingquarry
|
public |
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
|
2025-04-18 |
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squirrel
|
public |
Some QUIck Reconstruction to Resolve Evolutionary Links
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2025-04-18 |
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nail
|
public |
Profile Hidden Markov Model (pHMM) biological sequence alignment tool
|
2025-04-18 |
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hmftools-chord
|
public |
Predict HRD using somatic mutations contexts
|
2025-04-18 |
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perl-io-interactive
|
public |
Utilities for interactive I/O
|
2025-04-18 |
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vuegen
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public |
VueGen automates the creation of reports from bioinformatics outputs,
supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js,
Jupyter notebooks, and Streamlit web applications. Users simply
provide a directory with output files—such as plots, tables, networks,
Markdown text, and HTML files—and VueGen compiles them into a structured report.
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2025-04-18 |
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rdrpcatch
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public |
RNA virus RdRp sequence scanner.
|
2025-04-18 |
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vcfdist
|
public |
vcfdist: benchmarking phased germline variant calls in VCF format
|
2025-04-18 |
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gemma
|
public |
Linear mixed models (LMMs) for genome-wide association (GWA)
|
2025-04-18 |
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mimick
|
public |
Simulate linked-read data.
|
2025-04-18 |
|
gadma
|
public |
Genetic Algorithm for Demographic Inference
|
2025-04-18 |
|
ncbi-datasets-pyclient
|
public |
NCBI Datasets API
|
2025-04-18 |
|
flair
|
public |
Correction, isoform definition, and alternative splicing analysis of noisy reads (ONT and PacBio).
|
2025-04-18 |
|
scoring-matrices
|
public |
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
|
2025-04-18 |
|
dbcan
|
public |
Standalone version of dbCAN annotation tool for automated CAZyme annotation.
|
2025-04-18 |
|
amulety
|
public |
Python package to create embeddings of BCR amino acid sequences.
|
2025-04-18 |
|
syri
|
public |
Synteny and rearrangement identifier between whole-genome assemblies.
|
2025-04-18 |
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bioconda-repodata-patches
|
public |
generate tweaks to index metadata, hosted separately from anaconda.org index
|
2025-04-18 |
|
zol
|
public |
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters.
|
2025-04-17 |
|
gfftk
|
public |
GFFtk: genome annotation GFF3 tool kit
|
2025-04-17 |
|
sigprofilermatrixgenerator
|
public |
SigProfiler matrix generator tool.
|
2025-04-17 |
|
trgt
|
public |
Tandem repeat genotyping and visualization from PacBio HiFi data
|
2025-04-17 |
|
libcarna
|
public |
Real-time 3D visualization of biomedical data and beyond
|
2025-04-17 |
|
roadies
|
public |
Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES).
|
2025-04-16 |
|
captus
|
public |
Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data.
|
2025-04-16 |
|
r-ukbrapr
|
public |
R functions to use in the UK Biobank Research Analysis Platform (RAP)
|
2025-04-16 |
|
ncbi-stxtyper
|
public |
StxTyper identifies and types Stx operons from assembled genomic sequence.
|
2025-04-16 |
|
primer3
|
public |
Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it.
|
2025-04-16 |
|
grz-cli
|
public |
Tool for validation, encryption and upload of MV submissions to GDCs.
|
2025-04-16 |
|
annonars
|
public |
Genome annotation based on Rust and RocksDB.
|
2025-04-16 |
|
mehari
|
public |
VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust.
|
2025-04-16 |
|
muat
|
public |
A package for Mutation Attention Tool
|
2025-04-16 |
|
fastp
|
public |
A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...).
|
2025-04-16 |
|
atlas
|
public |
ATLAS: Analysis Tools for Ancient and Low-depth Samples
|
2025-04-16 |
|
aster
|
public |
Accurate Species Tree EstimatoR series; a family of optimation algorithms
for species tree inference implemented in C++
|
2025-04-16 |
|
augustus
|
public |
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
|
2025-04-16 |
|
snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-04-16 |
|
snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-04-16 |
|
tower-cli
|
public |
The Tower CLI an interface to Nextflow Tower via the CLI
|
2025-04-16 |
|
panaln
|
public |
Indexing pangenome for read alignment.
|
2025-04-16 |
|
pigpen
|
public |
A package to quantify RNA localization using OINC-seq data
|
2025-04-16 |
|
cdskit
|
public |
CDSKIT processes protein-coding sequences.
|
2025-04-16 |
|
lastz
|
public |
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
|
2025-04-16 |
|
caspeak
|
public |
A pipeline for finding non-reference mobile element insertions
|
2025-04-16 |
