| Package Name | Access | Summary | Updated |
|---|---|---|---|
| r-spp | public | Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) <DOI:10.1038/nbt.1508>]. | 2025-09-16 |
| fraggenescan | public | FragGeneScan is an application for finding (fragmented) genes in short reads. | 2025-09-16 |
| elprep | public | elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4. | 2025-09-16 |
| bamm | public | Metagenomics-focused BAM file manipulation | 2025-09-16 |
| perl-math-base-convert | public | Very fast base to base conversion. | 2025-09-16 |
| gmap | public | Genomic mapping and alignment program for mRNA and EST sequences. | 2025-09-15 |
| sonicparanoid | public | SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models | 2025-09-15 |
| perl-mime-types | public | Definition of MIME types | 2025-09-15 |
| perl-libwww-perl | public | The World-Wide Web library for Perl. | 2025-09-14 |
| vcf2maf | public | Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms. | 2025-09-13 |
| eggnog-mapper | public | Fast genome-wide functional annotation through orthology assignment. | 2025-09-13 |
| gseapy | public | Gene Set Enrichment Analysis in Python. | 2025-09-13 |
| perl-excel-writer-xlsx | public | Create a new file in the Excel 2007+ XLSX format. | 2025-09-13 |
| gtdbtk | public | A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. | 2025-09-12 |
| perl-mce | public | Many-Core Engine for Perl providing parallel processing capabilities | 2025-09-10 |
| perl-image-exiftool | public | ExifTool is a platform-independent Perl library plus a command-line application for reading, writing and editing meta information in a wide variety of files. | 2025-09-10 |
| addrg | public | No Summary | 2025-09-10 |
| rascaf | public | Scaffolding with RNA-seq read alignment. | 2025-09-10 |
| pathoscope | public | Species identification and strain attribution with unassembled sequencing data | 2025-09-10 |
| splicemap | public | Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. | 2025-09-10 |
| hardklor | public | Analyze mass spectra | 2025-09-10 |
| gxformat2 | public | Galaxy Workflow Format 2 Descriptions. | 2025-09-10 |
| antismash | public | antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell. | 2025-09-09 |
| trimadap | public | Fast but inaccurate adapter trimmer for Illumina reads. | 2025-09-09 |
| fermikit | public | No Summary | 2025-09-09 |
