Tool Library list page for genomics topic with tag ENCODE
Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately aligning long (several kilobases) reads that are emerging from the third-generation sequencing technologies.
UCSC genome browser 'kent' bioinformatic utilities
These are only the command line bioinformatic utilities
from the kent source tree.
"Python scripts for running ENCODE atac-seq pipeline."
"Python scripts for running ENCODE chip-seq-pipeline2"