Fast alignment and preprocessing of chromatin profiles with Chromap.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 34772935.
- Also identified by DOI 10.1038/s41467-021-26865-w and PMC identifier 8589834.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Chromatin
- Genomics