n³ The unorthodox terminal file manager

Toolkit for processing sequences in FASTA/Q formats

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

A python extension for quick access to bigWig and bigBed files

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Merging paired-end reads and removing adapters

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Python bindings to UCSC BigWig and BigBed library

A modified Ziggurat Algorithm for efficiently generating exponentially- and normally-distributed PseudoRandom Numbers (PRNs).