| Package Name | Access | Summary | Updated |
|---|---|---|---|
| superintervals | public | Rapid interval intersections. | 2025-07-28 |
| ensembl-py | public | Ensembl Python base library | 2025-07-28 |
| mupbwt | public | A light pbwt-based index | 2025-07-28 |
| diamond | public | Accelerated BLAST compatible local sequence aligner. | 2025-07-28 |
| hmftools-pave | public | PAVE annotates SNV/MNV/INDEL calls with consequence on corresponding genes, transcripts, and proteins. | 2025-07-28 |
| hmftools-cobalt | public | Calculate read-depth counts and GC ratios to use in PURPLE. | 2025-07-28 |
| hmftools-isofox | public | Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples. | 2025-07-28 |
| readfq | public | A high-speed tool to calculate reads number and total base count in FASTQ file, forked from Li Heng's original version | 2025-07-28 |
| kmergenie | public | KmerGenie estimates the best k-mer length for genome de novo assembly | 2025-07-28 |
| ribotin | public | Ribosomal DNA assembly tool. | 2025-07-28 |
| maker | public | MAKER is a portable and easily configurable genome annotation pipeline. | 2025-07-28 |
| mp-est | public | Maximum Pseudo-likelihood Estimation of Species Trees | 2025-07-28 |
| winnowmap | public | Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. | 2025-07-28 |
| graphaligner | public | Sequence to graph aligner for long reads | 2025-07-27 |
| plass | public | Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs | 2025-07-27 |
| spacepharer | public | SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts | 2025-07-27 |
| alphafill | public | Transplant missing compounds to the AlphaFold models | 2025-07-27 |
| mrtrix3 | public | A set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density | 2025-07-27 |
| fibertools-rs | public | Mitchell Vollger's rust tools for fiberseq data. | 2025-07-27 |
| hmftools-orange | public | ORANGE summarizes the key outputs from all algorithms in the Hartwig suite. | 2025-07-27 |
| mmseqs2 | public | MMseqs2: ultra fast and sensitive sequence search and clustering suite | 2025-07-27 |
| checkatlas | public | One liner tool to check the quality of your single-cell atlases. | 2025-07-26 |
| viloca | public | VILOCA is a tool to analyse short- and long-read sequencing viral samples. It provides mutation calls and local haplotypes. | 2025-07-25 |
| bandwagon | public | Simulate DNA band patterns for gel migration experiments | 2025-07-24 |
| met4j | public | Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks | 2025-07-24 |
