This tar file includes the bowtie2 index for the human genome build GRCh38. We use the UCSC hg38 version of the genome, corresponsing to GRCh38/GCA_000001405.15 including the 25 assembled chromosomes (1-22, X, Y, M), the 127 unplaced contigs, the 42 unlocalized contigs, but excluding the 261 alternative haplotypes. The assembly also includes the Epstein-Barr virus (EBV) genome. This is the same reference as used by the ENCODE Consortium for data processing: https://www.encodeproject.org/data-standards/reference-sequences/ .