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
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.
Topics & Concepts
ChromatinBottleneckPreprocessorComputational biologyComputer scienceGenomicsPipeline (software)ChIP-sequencingWorkflowGenomeBiologyNucleosomeGeneticsArtificial intelligenceDNAGeneDatabaseEmbedded systemProgramming languageGenomics and Chromatin DynamicsSingle-cell and spatial transcriptomicsGenomics and Phylogenetic Studies