@article {Zhang2021.06.18.448995, author = {Haowen Zhang and Li Song and Xiaotao Wang and Haoyu Cheng and Chenfei Wang and Clifford A. Meyer and Tao Liu and Ming Tang and Srinivas Aluru and Feng Yue and X. Shirley Liu and Heng Li}, title = {Fast alignment and preprocessing of chromatin profiles with Chromap}, elocation-id = {2021.06.18.448995}, year = {2021}, doi = {10.1101/2021.06.18.448995}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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{\textquoteright} CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.Competing Interest StatementX.S.L. is a cofounder, board and SAB member of GV20 Oncotherapy, SAB of 3DMed Care, consultant for Genentech, stockholder of BMY, TMO, WBA, ABT, ABBV, and JNJ, and received research funding from Takeda and Sanofi. H.L. is a consultant of Integrated DNA Technologies and on the SAB of Sentieon, Innozeen and BGI.}, URL = {https://www.biorxiv.org/content/early/2021/06/18/2021.06.18.448995}, eprint = {https://www.biorxiv.org/content/early/2021/06/18/2021.06.18.448995.full.pdf}, journal = {bioRxiv} }