| Package Name | Access | Summary | Updated |
|---|---|---|---|
| dragmap | public | Dragmap is the Dragen mapper/aligner Open Source Software. | 2025-09-30 |
| art_modern | public | Modernized ART simulator of diverse Next-Generation Sequencing reads | 2025-09-30 |
| trycycler | public | Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. | 2025-09-30 |
| desalt | public | De Bruijn graph-based Spliced Aligner for Long Transcriptome reads | 2025-09-30 |
| scallop2 | public | A reference-based transcript assembler optimized for paired-/multiple-end RNA-seq data. | 2025-09-30 |
| rnabridge-align | public | A tool to construct the alignments of entire fragments given the alignments of paired-end reads. | 2025-09-30 |
| wade | public | WADE provides a flexible and customizable method to extract specific genes from a large number of genomes at once. | 2025-09-30 |
| breakinator | public | Detection of foldback and chimeric read artifacts in PAF files. | 2025-09-30 |
| liana | public | LIANA+: a one-stop-shop framework for cell-cell communication. | 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 |
| hyplas | public | Hybrid long- short- plasmid assembler. | 2025-09-29 |
| nextstrain-cli | public | The Nextstrain command-line interface (CLI). | 2025-09-29 |
| phykit | public | PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data. | 2025-09-29 |
| apscale | public | Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data. | 2025-09-29 |
| hifi_trimmer | public | hifi_trimmer is a tool for filtering and trimming extraneous adapter hits from a HiFi read set using a BLAST search. | 2025-09-29 |
| r-hmm | public | Functions for hidden Markov Models (HMM). | 2025-09-29 |
| pysradb | public | Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO | 2025-09-29 |
| cytoscape | public | Cytoscape: an open source platform for network analysis and visualization. | 2025-09-29 |
| afragmenter | public | Schema-free, tunable protein domain segmentation tool for AlphaFold structures | 2025-09-29 |
| plassembler | public | Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates. | 2025-09-29 |
| captus | public | Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data. | 2025-09-29 |
| sopa | public | Spatial-omics pipeline and analysis. | 2025-09-29 |
