| Package Name | Access | Summary | Updated |
|---|---|---|---|
| shovill | public | Microbial assembly pipeline for Illumina paired-end reads | 2025-10-02 |
| mccortex | public | De novo genome assembly and multisample variant calling | 2025-10-01 |
| rnablueprint | public | The RNAblueprint library solves the problem of uniformly sampling RNA/DNA sequences compatible to multiple structural constraints and sequence constraints. | 2025-10-01 |
| hyphy | public | An open-source software package for comparative sequence analysis using stochastic evolutionary models. | 2025-10-01 |
| cyvcf2 | public | A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files. | 2025-10-01 |
| snakemake-minimal | public | A popular workflow management system aiming at full in-silico reproducibility. | 2025-10-01 |
| snakemake | public | A popular workflow management system aiming at full in-silico reproducibility. | 2025-10-01 |
| rnaz | public | predicting structural noncoding RNAs | 2025-09-30 |
| segemehl | public | Short read mapping with gaps | 2025-09-30 |
| rainbow | public | Efficient tool for clustering and assembling short reads, especially for RAD | 2025-09-30 |
| stacks | public | Stacks is a software pipeline for building loci from short-read sequences. | 2025-09-30 |
| genomepy | public | Install and use genomes & gene annotations the easy way! | 2025-09-30 |
| kraken | public | Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. | 2025-09-30 |
| snpeff | public | Genetic variant annotation and effect prediction toolbox | 2025-09-30 |
| rnacode | public | RNAcode - Analyze the protein coding potential in multiple sequence alignments RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques. | 2025-09-30 |
| sweepfinder2 | public | The BWA read mapper. | 2025-09-29 |
| r-structssi | public | Performs multiple testing corrections that take specific structure of hypotheses into account. | 2025-09-29 |
| pysradb | public | Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO | 2025-09-29 |
| gatk4 | public | Genome Analysis Toolkit (GATK4) | 2025-09-29 |
| perl-extutils-parsexs | public | Converts Perl XS code into C code. | 2025-09-27 |
| spades | public | SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. | 2025-09-27 |
| randfold | public | No Summary | 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 |
| 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 |
