| Package Name | Access | Summary | Updated |
|---|---|---|---|
| clair3-illumina | public | Clair3 with libraries to support variant calling using Illumina short-reads. Version in sync with Clair3. | 2025-08-01 |
| clair3 | public | Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration. | 2025-08-01 |
| seqfu | public | DNA sequence utilities | 2025-08-01 |
| oligomap | public | Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. | 2025-08-01 |
| stereogene | public | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data | 2025-08-01 |
| sorted_nearest | public | Find nearest interval. | 2025-08-01 |
| metabolishmm | public | Constructing phylogenies and performing functional annotations with HMM markers. | 2025-08-01 |
| ngseqbasic | public | Basic ChIP/DNaseI/ATAC analysis - from FASTQ to visualisation of tracks, in one command. | 2025-08-01 |
| geno2phenotb | public | Prediction of Mycobacterium tuberculosis drug resistance from WGS data | 2025-08-01 |
| tortoize | public | Application to calculate ramachandran z-scores | 2025-08-01 |
| bioemu | public | Biomolecular emulator for scalable emulation of protein equilibrium ensembles with generative deep learning | 2025-08-01 |
| hapcut2 | public | Tools for haplotype assembly from sequence data | 2025-08-01 |
| spacerextractor | public | Extract CRISPR spacers from metagenome short reads. | 2025-08-01 |
| libsequence | public | A C++ class library for evolutionary genetics. | 2025-08-01 |
| genometools-genometools | public | GenomeTools genome analysis system. | 2025-07-31 |
| bcbio-gff | public | A Python library to read and write Generic Feature Format (GFF). | 2025-07-31 |
| gndiff | public | GNdiff compares scientific names from two files | 2025-07-31 |
| ezaai | public | EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis and dendrogram representation. | 2025-07-31 |
| cyvcf2 | public | A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files | 2025-07-31 |
| genome-uploader | public | Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). | 2025-07-31 |
| bifrost-httr | public | Pre-release version for testing purposes only | 2025-07-31 |
| nomadic | public | Mobile sequencing and analysis in real-time | 2025-07-31 |
| changeo | public | A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data. | 2025-07-31 |
| ntcard | public | Estimating k-mer coverage histogram of genomics data | 2025-07-31 |
| cuttlefish | public | Construction of the compacted de Bruijn graph efficiently | 2025-07-31 |
