| Package Name | Access | Summary | Updated |
|---|---|---|---|
| polypolish | public | Polishing genome assemblies with short reads. | 2025-08-28 |
| popscle | public | A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools | 2025-08-28 |
| bedtk | public | Bedtk is a set of simple tools to process BED files. | 2025-08-28 |
| scmidas | public | A torch-based integration method for single-cell multi-omic data. | 2025-08-28 |
| myloasm | public | myloasm - high-resolution metagenome assembly for (noisy) long reads | 2025-08-28 |
| orthofinder | public | Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy! | 2025-08-28 |
| vcontact3 | public | Viral Contig Automatic Clustering and Taxonomy. | 2025-08-28 |
| repeatmasker | public | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | 2025-08-28 |
| viralmsa | public | Reference-guided multiple sequence alignment of viral genomes | 2025-08-28 |
| vapor | public | VAPOR is a tool for classification of Influenza samples from short read sequence data for further bioinformatics analysis. | 2025-08-28 |
| olivar | public | Olivar PCR tiling design | 2025-08-28 |
| freyja | public | Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics. | 2025-08-28 |
| arborator | public | Arborator: Simplifying operationalized pathogen surveillance and outbreak detection. | 2025-08-28 |
| pgscatalog.calc | public | Libraries and applications for working with calculated polygenic scores. | 2025-08-28 |
| gubbins | public | Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. | 2025-08-28 |
| magmax | public | MAGmax is a robust tool for dereplicating MAGs through bin merging and reassembly. | 2025-08-28 |
| r-flanders | public | Fast colocalization using AnnData objects in R | 2025-08-28 |
| r-presto | public | Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment. | 2025-08-28 |
| coot-headless | public | Coot Headless API - Software for macromolecular model building. | 2025-08-28 |
| allelecodes | public | Allele Code Assignment Algorithm for cgMLST schemes | 2025-08-27 |
| pysradb | public | Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO | 2025-08-27 |
| jcvi | public | Python utility libraries on genome assembly, annotation, and comparative genomics. | 2025-08-27 |
| seismic-rna | public | SEISMIC-RNA software by the Rouskin Lab. | 2025-08-26 |
| probe | public | Evaluate and visualize protein interatomic packing | 2025-08-26 |
| pyani-plus | public | Whole-genome classification of microbes using Average Nucleotide Identity and similar methods. | 2025-08-26 |
