| Package Name | Access | Summary | Updated |
|---|---|---|---|
| zerone | public | Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. | 2025-09-16 |
| yass | public | YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format. | 2025-09-16 |
| 10x_bamtofastq | public | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis | 2025-09-16 |
| enhjoerning | public | A tool for computing statistics on short read alignments. | 2025-09-16 |
| samshee | public | A schema-agnostic parser and writer for illumina sample sheets v2. | 2025-09-16 |
| clincnv | public | Copy number variation detection for clinical sequencing. | 2025-09-16 |
| mpralib | public | Library to analyze count data of MPRA experiments. | 2025-09-16 |
| 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 |
| oxbow | public | Read genomic file formats into data frames and more. | 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 |
