Table 4.
Peak Calling Tools
| Languages | Notes | Docs | Citation | |
|---|---|---|---|---|
| F-Seq | Java | Can be used as general peak caller to identify regions of open chromatin. | ++ |
Boyle et al. (2008) Last updated: 2016 |
| Genrich | C | Peak caller for genomic enrichment assays with specific ATAC-seq mode. | +++ | unpublished Last updated: 2020 |
| HMMRATAC | Java | Identify nucleosome positioning and leverage ATAC-seq specific read outs to call peaks. | +++ |
Tarbell & Liu (2019) Last updated: 2020 |
| Hotspot2 | C++ | Identify significantly enriched genomic regions. | ++ | Unpublished Last updated: 2019 |
| HOMER | Perl; C++ | Suite of tools that include the ability to call peaks from DNA enrichment assays. | +++ |
Heinz et al. (2010) Last updated: 2010 |
| MACS2 | Python | Specifically designed for CHiP-seq but broadly applicable to any DNA enrichment assay to call peaks. | +++ |
Zhang et al. (2020) Last updated: 2020 |
| PeaKDEck | Perl | Peak calling program for DNase-seq data. | +++ |
McCarthy & O’Callaghan (2014) Last updated: 2014 |