| Package Name | Access | Summary | Updated |
|---|---|---|---|
| locidex | public | Locidex: Common search engine for similarity based typing applications. | 2025-08-28 |
| crass | public | Crass (The CRISPR Assembler) is a program that searches through raw metagenomic reads for Clustered Regularly Interspersed Short Palindromic Repeats | 2025-08-28 |
| phcue-ck | public | phcue-ck (pronounced "F-Q-Seek") is a simple tool to get FTP urls for FASTQ files on ENA. | 2025-08-28 |
| usearch | public | USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. | 2025-08-28 |
| sistem | public | A tool for simulating tumor growth, metastasis, and DNA-seq data. | 2025-08-28 |
| damidseq_pipeline | public | An automated pipeline for processing DamID sequencing datasets. | 2025-08-28 |
| phist | public | Phage-Host Interaction Search Tool. | 2025-08-28 |
| piret | public | A tool for conducting RNA seq analysis. | 2025-08-28 |
| pin_hic | public | A Hi-C scaffolding method | 2025-08-28 |
| 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 |
