Table 1.

ENCODE DCC implemented uniform processing pipelines.

Assay	GitHub repository
ChIP-seq	https://github.com/ENCODE-DCC/chip-seq-pipeline2
ATAC-seq	https://github.com/ENCODE-DCC/atac-seq-pipeline
DNase-seq	https://github.com/ENCODE-DCC/dnase-seq-pipeline
RNA-seq (inc. micro)	https://github.com/ENCODE-DCC/rna-seq-pipeline
long read RNA-seq	https://github.com/ENCODE-DCC/long-read-rna-pipeline
WGBS	https://github.com/ENCODE-DCC/wgbs-pipeline
Hi-C	https://github.com/ENCODE-DCC/hic-pipeline