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Fast alignment and preprocessing of chromatin profiles with Chromap

Author

Listed:
  • Haowen Zhang

    (Georgia Institute of Technology)

  • Li Song

    (Dana-Farber Cancer Institute
    Harvard T.H. Chan School of Public Health)

  • Xiaotao Wang

    (Northwestern University)

  • Haoyu Cheng

    (Dana-Farber Cancer Institute
    Harvard Medical School)

  • Chenfei Wang

    (Dana-Farber Cancer Institute
    Harvard T.H. Chan School of Public Health)

  • Clifford A. Meyer

    (Dana-Farber Cancer Institute
    Harvard T.H. Chan School of Public Health
    Dana-Farber Cancer Institute)

  • Tao Liu

    (Roswell Park Comprehensive Cancer Center)

  • Ming Tang

    (Dana-Farber Cancer Institute)

  • Srinivas Aluru

    (Georgia Institute of Technology
    Georgia Institute of Technology)

  • Feng Yue

    (Northwestern University
    Robert H. Lurie Comprehensive Cancer Center of Northwestern University)

  • X. Shirley Liu

    (Dana-Farber Cancer Institute
    Harvard T.H. Chan School of Public Health
    Dana-Farber Cancer Institute)

  • Heng Li

    (Dana-Farber Cancer Institute
    Harvard Medical School)

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.

Suggested Citation

  • 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, 2021. "Fast alignment and preprocessing of chromatin profiles with Chromap," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26865-w
    DOI: 10.1038/s41467-021-26865-w
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    References listed on IDEAS

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    1. Job Dekker & Andrew S. Belmont & Mitchell Guttman & Victor O. Leshyk & John T. Lis & Stavros Lomvardas & Leonid A. Mirny & Clodagh C. O’Shea & Peter J. Park & Bing Ren & Joan C. Ritland Politz & Jay S, 2017. "The 4D nucleome project," Nature, Nature, vol. 549(7671), pages 219-226, September.
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    3. Jason D. Buenrostro & Beijing Wu & Ulrike M. Litzenburger & Dave Ruff & Michael L. Gonzales & Michael P. Snyder & Howard Y. Chang & William J. Greenleaf, 2015. "Single-cell chromatin accessibility reveals principles of regulatory variation," Nature, Nature, vol. 523(7561), pages 486-490, July.
    4. Job Dekker & Andrew S. Belmont & Mitchell Guttman & Victor O. Leshyk & John T. Lis & Stavros Lomvardas & Leonid A. Mirny & Clodagh C. O’Shea & Peter J. Park & Bing Ren & Joan C. Ritland Politz & Jay S, 2017. "Correction: Corrigendum: The 4D nucleome project," Nature, Nature, vol. 552(7684), pages 278-278, December.
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    Cited by:

    1. Chunhong Yu & Xiaoyun Lei & Fang Chen & Song Mao & Lu Lv & Honglu Liu & Xueying Hu & Runhan Wang & Licong Shen & Na Zhang & Yang Meng & Yunfan Shen & Jiale Chen & Pishun Li & Shi Huang & Changwei Lin , 2022. "ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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