Nature CommunicationsBioinformaticsPeer-reviewed journal article
Fast alignment and preprocessing of chromatin profiles with Chromap
Haowen ZhangiD, Li SongiD, Xiaotao WangiD, Haoyu ChengiD, Chenfei WangiD, Clifford A. MeyeriD, Tao LiuiD, Ming TangiD, Srinivas AluruiD, Feng YueiD, X. Shirley LiuiD, Heng LiiD
Abstract
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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