| Package Name | Access | Summary | Updated |
|---|---|---|---|
| cosigt | public | Cosigt (COsine SImilarity-based GenoTyper) | 2025-09-16 |
| agtools | public | agtools: A Software Framework to Manipulate Assembly Graphs | 2025-09-16 |
| genepop | public | Population Genetic Data Analysis package. | 2025-09-16 |
| snp-sites | public | Finds SNP sites from a multi-FASTA alignment file. | 2025-09-16 |
| clever-toolkit | public | The clever toolkit (CTK) is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads. | 2025-09-16 |
| phispy | public | Prophage finder using multiple metrics | 2025-09-16 |
| 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 |
| ruranges | public | Rust-backed interval kernels exposed to Python/NumPy. | 2025-09-16 |
| egap | public | EGAP pipeline for genome assembly and QC analysis | 2025-09-16 |
| bamrescue | public | Utility to check BAM files for corruption and repair by skipping corrupted BGZF blocks | 2025-09-15 |
| kf2vec | public | K-mer frequency to vector tool. | 2025-09-15 |
| quick-variants | public | Fast and accurate genetic variant identification | 2025-09-15 |
| nerpa | public | A tool for discovering biosynthetic gene clusters of nonribosomal peptides | 2025-09-15 |
| ppanggolin | public | PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph. | 2025-09-15 |
| gmap | public | Genomic mapping and alignment program for mRNA and EST sequences. | 2025-09-15 |
| groopm | public | Metagenomic binning suite | 2025-09-15 |
| sonicparanoid | public | SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models | 2025-09-15 |
| sdeper | public | Spatial Deconvolution method with Platform Effect Removal | 2025-09-15 |
| ampliconsuite | public | An end-to-end wrapper for focal amplification analysis from whole-genome sequencing using AmpliconArchitect and associated tools. | 2025-09-15 |
| mutamr | public | Stripped down tool for generation of annotated vcf from paired-end reads in a CPHL. | 2025-09-15 |
| mirscore | public | miRScore: A rapid and precise microRNA validation tool | 2025-09-15 |
