| Package Name | Access | Summary | Updated |
|---|---|---|---|
| nwalign3 | public | Updated version of nwalign (Needleman-Wunsch global sequence alignment) with Python 3.x compatibility. | 2025-09-30 |
| cellsnp-lite | public | Efficient genotyping bi-allelic SNPs on single cells | 2025-09-30 |
| unimap | public | Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. | 2025-09-30 |
| segemehl | public | Short read mapping with gaps | 2025-09-30 |
| nanomotif | public | Identifying methlyation motifs in nanopore data. | 2025-09-30 |
| rainbow | public | Efficient tool for clustering and assembling short reads, especially for RAD | 2025-09-30 |
| varlociraptor | public | Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control. | 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 |
| ms2rescore-rs | public | Rust functionality for the MS²Rescore package | 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 |
| kmer-jellyfish | public | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence | 2025-09-30 |
| libcifpp | public | Library containing code to manipulate mmCIF and PDB files. | 2025-09-30 |
| nf-test | public | nf-test is a simple test framework for Nextflow pipelines. | 2025-09-30 |
| metawrap-mg | public | MetaWRAP is a pipeline for genome-resolved metagenomic data analysis | 2025-09-30 |
| dragmap | public | Dragmap is the Dragen mapper/aligner Open Source Software. | 2025-09-30 |
| epimetheus-py | public | CLI tool for fast lookup in pileup for motif methylation. | 2025-09-30 |
| varpubs | public | Tool for finding PubMed evidence on genetic variants and generating LLM-based summaries | 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 |
| scallop | public | Scallop is a reference-based transcriptome assembler for RNA-seq | 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 |
