Fast alignment and preprocessing of chromatin profiles with Chromap

Haowen Zhang, Li Song, Xiaotao Wang, Haoyu Cheng, Chenfei Wang, Clifford A. Meyer, Tao Liu, Ming Tang, Srinivas Aluru, Feng Yue, X. Shirley Liu () and Heng Li ()
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Haowen Zhang: Georgia Institute of Technology
Li Song: Dana-Farber Cancer Institute
Xiaotao Wang: Northwestern University
Haoyu Cheng: Dana-Farber Cancer Institute
Chenfei Wang: Dana-Farber Cancer Institute
Clifford A. Meyer: Dana-Farber Cancer Institute
Tao Liu: Roswell Park Comprehensive Cancer Center
Ming Tang: Dana-Farber Cancer Institute
Srinivas Aluru: Georgia Institute of Technology
Feng Yue: Northwestern University
X. Shirley Liu: Dana-Farber Cancer Institute
Heng Li: Dana-Farber Cancer Institute

Nature Communications, 2021, vol. 12, issue 1, 1-6

Abstract: 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’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.

Date: 2021
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DOI: 10.1038/s41467-021-26865-w

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