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; Heng Li

doi:10.1038/s41467-021-26865-w

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^*, Heng Li^*

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

63 Scopus citations

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.

Original language	English (US)
Article number	6566
Journal	Nature communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-26865-w
State	Published - Dec 2021

Funding

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. 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].

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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AU - Tang, Ming

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Fast alignment and preprocessing of chromatin profiles with Chromap

Abstract

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ASJC Scopus subject areas

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