BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

We present a tool for processing NGS DNA-seq BAM files to quantify peaks and create coverage tracks from ChIP-seq, NS-seq, ATAC-seq, OK-seq, END-seq and replication timing data BAMscale is a one-step tool that processes DNA sequencing datasets from chromatin binding (ChIP-seq) and chromatin state changes (ATAC-seq, END-seq) experiments to DNA replication data (OK-seq, NS-seq and replication timing). The outputs include normalized peak scores in text format and scaled coverage tracks (BigWig) which are directly accessible to data visualization programs. BAMscale (available at https://github.com/ncbi/BAMscale) effectively processes large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools. This series includes re-analyzed data from: GSE101512 (ATAC-seq on peripheral blood), GSE116321 (Mouse_Okseq_ENDseq_RepliSeq on Activated primary B cells), ERR2760956 (OK-seq on K562) and GSE122489 (RNA-seq).