@article{774f69f841d24ab6b36154b92c6ba7f7,
title = "Fast alignment and preprocessing of chromatin profiles with Chromap",
abstract = "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{\textquoteright} CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.",
author = "Haowen Zhang and Li Song and Xiaotao Wang and Haoyu Cheng and Chenfei Wang and Meyer, {Clifford A.} and Tao Liu and Ming Tang and Srinivas Aluru and Feng Yue and Liu, {X. Shirley} and Heng Li",
note = "Funding Information: The authors declare the following competing interests. X.S.L. is a cofounder, board member, SAB member, and consultant of GV20 Oncotherapy and its subsidiaries; stockholder of BMY, TMO, WBA, ABT, ABBV, and JNJ; and received research funding from Takeda, Sanofi, Bristol Myers Squibb, and Novartis. H.L. is a consultant of Integrated DNA Technologies and on the SAB of Sentieon and Innozeen. Funding Information: We acknowledge the following funding sources for supporting this work: Breast Cancer Foundation [BCRF-20-100 to XSL] and National Institute of Health [R01HG010040, R01HG011139, and U01CA226196 to HL]. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
doi = "10.1038/s41467-021-26865-w",
language = "English (US)",
volume = "12",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}