| Package Name | Access | Summary | Updated |
|---|---|---|---|
| spades | public | SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. | 2025-09-27 |
| dysgu | public | A collection of tools for calling structural variants using short or long reads. | 2025-09-27 |
| randfold | public | No Summary | 2025-09-26 |
| oxbow | public | Read genomic file formats into data frames and more. | 2025-09-26 |
| prinseq-plus-plus | public | PRINSEQ++ - Multi-threaded C++ sequence cleaning | 2025-09-26 |
| maxbin2 | public | MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. | 2025-09-26 |
| corset | public | Software for clustering de novo assembled transcripts and counting overlapping reads. | 2025-09-26 |
| psiclass | public | Simultaneous multi-sample transcript assembler for RNA-seq data | 2025-09-26 |
| ephemeris | public | Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows. | 2025-09-26 |
| spaln | public | Map and align a set of cDNA/EST or protein sequences onto a genome. | 2025-09-26 |
| parnas | public | Representative taxon sampling from phylogenetic trees | 2025-09-26 |
| beacon2-ri-tools | public | Package of tools designed to simplify the population of a Beacon v2 mongoDB database | 2025-09-26 |
| lca | public | LCA - Lowest Common Ancestor calculation tool | 2025-09-26 |
| kma | public | KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | 2025-09-26 |
| lodei | public | Analyze differentially edited A-to-I regions in two sets of RNA-seq samples. | 2025-09-26 |
| ensembl-vep | public | Ensembl Variant Effect Predictor | 2025-09-26 |
| clustalo | public | Latest version of Clustal: a multiple sequence alignment program for DNA or proteins | 2025-09-26 |
| mehari | public | VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust. | 2025-09-26 |
| emboss | public | The European Molecular Biology Open Software Suite | 2025-09-26 |
| consel | public | CONSEL calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection | 2025-09-26 |
| pybedlite | public | Lightweight python classes for interfacing with bed intervals. | 2025-09-26 |
| pybwa | public | Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa. | 2025-09-26 |
| pm4ngs | public | PM4NGS generates a standard organizational structure for Next Generation Sequencing (ngs) data analysis. | 2025-09-26 |
| pharokka | public | Fast Phage Annotation Program | 2025-09-25 |
| kmc | public | Tools for efficient k-mer counting and filtering of reads based on k-mer content. | 2025-09-25 |
