RNA-seq aligner

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Toolkit for processing sequences in FASTA/Q formats

bedtools - the swiss army knife for genome arithmetic

🔬 BEDOPS: high-performance genomic feature operations

Single-cell Transcriptome and Regulome Analysis Pipeline

Detecting sites of genomic enrichment

UCSC command line bioinformatic utilities

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Package for including repetitive regions in peak calling from ChIP-seq datasets