Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
☆328Mar 16, 2025Updated 11 months ago
Alternatives and similar repositories for pybedtools
Users that are interested in pybedtools are comparing it to the libraries listed below
Sorting:
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆880Feb 2, 2026Updated 3 weeks ago
- Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl☆400Aug 13, 2025Updated 6 months ago
- GFF and GTF file manipulation and interconversion☆314Jan 26, 2026Updated last month
- bedtools - the swiss army knife for genome arithmetic☆1,022Mar 11, 2025Updated 11 months ago
- cython + htslib == fast VCF and BCF processing☆429Updated this week
- Performant Pythonic GenomicRanges☆494Jan 27, 2026Updated last month
- Efficient pythonic random access to fasta subsequences☆482Sep 3, 2025Updated 5 months ago
- Tools to process and analyze deep sequencing data.☆752Jul 23, 2025Updated 7 months ago
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆195Feb 1, 2026Updated 3 weeks ago
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆15Feb 13, 2018Updated 8 years ago
- python module to plot beautiful and highly customizable genome browser tracks☆864Jul 10, 2024Updated last year
- Parsing tools for GTF (gene transfer format) files☆127Feb 27, 2025Updated last year
- Python library to handle Gene Ontology (GO) terms☆877Dec 18, 2025Updated 2 months ago
- A python extension for quick access to bigWig and bigBed files☆239Jan 14, 2026Updated last month
- BEDOPS: high-performance genomic feature operations☆360Apr 29, 2025Updated 9 months ago
- Count bases in BAM/CRAM files☆324Jan 31, 2022Updated 4 years ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- Cutadapt removes adapter sequences from sequencing reads☆572Jan 12, 2026Updated last month
- a python package for fast random access to sequences from plain and gzipped FASTA/Q files☆290Jan 16, 2026Updated last month
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,421Updated this week
- Scripts, utilities and programs for genomic bioinformatics.☆83Nov 13, 2025Updated 3 months ago
- A cool place to store your Hi-C☆231Updated this week
- Pure-python implementation of UCSC liftOver genome coordinate conversion☆101Feb 8, 2024Updated 2 years ago
- Genomic interval operations on Pandas DataFrames☆189Feb 2, 2026Updated 3 weeks ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆822Feb 10, 2026Updated 2 weeks ago
- python access to UCSC genomes database☆136Aug 27, 2020Updated 5 years ago
- Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis☆23Jan 31, 2026Updated 3 weeks ago
- MACS -- Model-based Analysis of ChIP-Seq☆767Feb 20, 2026Updated last week
- annotate a VCF with other VCFs/BEDs/tabixed files☆397Aug 30, 2025Updated 5 months ago
- HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.☆129Apr 12, 2020Updated 5 years ago
- A collection of perl scripts for NGS analysis☆17Oct 2, 2024Updated last year
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 9 months ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆460Mar 13, 2024Updated last year
- A Variant Call Format reader for Python.☆417Sep 22, 2023Updated 2 years ago
- Very simple, pure python, BAM file reader☆79Feb 20, 2019Updated 7 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,292Jan 22, 2026Updated last month
- Gene Set Enrichment Analysis in Python☆690Dec 17, 2025Updated 2 months ago
- A Python package for exploring and analysing genetic variation data☆315Feb 1, 2026Updated 3 weeks ago