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

Nat Commun. 2021 Nov 12;12(1):6566. doi: 10.1038/s41467-021-26865-w.

Authors

Haowen Zhang^#¹, Li Song^#^{2

3}, Xiaotao Wang⁴, Haoyu Cheng^{2

5}, Chenfei Wang^{2

3}, Clifford A Meyer^{2

3

6}, Tao Liu⁷, Ming Tang², Srinivas Aluru^{1

8}, Feng Yue^{4

9}, X Shirley Liu^{10

11

12}, Heng Li^{13

14}

Affiliations

¹ School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
² Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
³ Harvard T.H. Chan School of Public Health, Boston, MA, USA.
⁴ Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
⁵ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
⁶ Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
⁷ Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
⁸ Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, GA, USA.
⁹ Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
¹⁰ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. xsliu.res@gmail.com.
¹¹ Harvard T.H. Chan School of Public Health, Boston, MA, USA. xsliu.res@gmail.com.
¹² Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. xsliu.res@gmail.com.
¹³ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. hli@ds.dfci.harvard.edu.
¹⁴ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. hli@ds.dfci.harvard.edu.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation Sequencing
Chromatin*
Computational Biology
Gene Expression Profiling / methods
Genomics / methods*
Humans
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA / methods
Single-Cell Analysis

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding