| sratoolkit | 2.5.7 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | Mar 25, 2025 | Public Domain |
| tabix | 0.2.6 | — | Mar 25, 2025 | — |
| pysam | 0.8.3 | — | Mar 25, 2025 | MIT |
| bedtools | 2.25.0 | A powerful toolset for genome arithmetic. | Mar 25, 2025 | GPL2 |
| pybedtools | 0.7.2 | — | Mar 25, 2025 | — |
| ucsc-bedgraphtobigwig | 323 | Convert a bedGraph file to bigWig format. | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| ucsc-wigtobigwig | 323 | Convert ascii format wig file (in fixedStep, variableStep | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| ucsc-bedtobigbed | 323 | Convert bed file to bigBed. (BigBed version: 4) | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| ucsc-fetchchromsizes | 323 | used to fetch chrom.sizes information from UCSC | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| bedgraphtobigwig | 0.0 | — | Mar 25, 2025 | — |
| functools32 | 3.2.3_2 | Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy. | Mar 25, 2025 | PSF license |
| wget | 3.2 | pure python download utility | Mar 25, 2025 | Public Domain |
| bedtobigbed | 0.0 | — | Mar 25, 2025 | — |
| samtools | 1.1 | Tools (written in C using htslib) for manipulating next-generation sequencing data | Jun 16, 2023 | MIT |
| python-wget | 3.2 | pure python download utility | Mar 25, 2025 | Public Domain |
| ucsc-bigbedtobed | 323 | Convert from bigBed to ascii bed format. | Mar 25, 2025 | varies; see http://genome.ucsc.edu/license |
| bleach | 1.4.2 | An easy whitelist-based HTML-sanitizing tool. | Mar 25, 2025 | Apache Software License |
| trackhub | 0.1.2 | \nCreate and manage UCSC track hubs from Python\n | Mar 25, 2025 | UNKNOWN |
| pyaml | 15.6.3 | PyYAML-based module to produce pretty and readable YAML-serialized data | Mar 25, 2025 | WTFPL |
| subread | 1.4.6p5 | High-performance read alignment, quantification, and mutation discovery | Jun 16, 2023 | GPLv3 |
| sh | 1.11 | Python subprocess interface | Mar 25, 2025 | MIT License |
| crossmap | 0.2.1 | Convert genomic coordiates between assemblies | Mar 25, 2025 | GPL |
| discover | 0.4.0 | Test discovery for unittest. Backported from Python 2.7 for Python 2.4+ | Mar 25, 2025 | BSD License |
| hubward | 0.1 | — | Mar 25, 2025 | — |
| vcversioner | 2.14.0.0 | Use version control tags to discover version numbers | Mar 25, 2025 | ISC License (ISCL) |
