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Fast alignment and preprocessing of chromatin profiles with Chromap

By Haowen Zhang, Li Song, Xiaotao Wang, Haoyu Cheng, Chenfei Wang, Clifford Meyer, Tao Liu, Ming Tang, Srinivas Aluru, Feng Yue, X. Shirley Liu, Heng Li

Posted 18 Jun 2021
bioRxiv DOI: 10.1101/2021.06.18.448995

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.

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