Fast alignment and preprocessing of chromatin profiles with Chromap.

As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles. As studies continue sequencing with deeper coverage, computational processing of these profiles has become increasingly resource consuming. Here the authors designed an efficient computational method called Chromap to align and preprocess high throughput sequencing data from chromatin profiling techniques, including ChIP-seq, Hi-C, or scATAC-seq, with a major decrease in runtime.