Table 2.
Raw ATAC-seq Data Processing Pipelines
| Language | Notes | Docs | Citation | |
|---|---|---|---|---|
| AIAP | Bash; R; Python | Optimized analysis with novel QC metrics | ++ |
Liu et al. (2019)
Last updated: 2019 |
| ATAC2GRN | Bash; Python | Parameter optimized ATAC-seq pipeline | + | Pranzatelli, Michael, & Chiorini (2018) |
| Last updated: 2018 | ||||
| ATAC-pipe | Python; R | Analysis pipeline for ATAC-seq data including TF footprinting; cell-type classification; and regulatory network creation | +++ | Zuo et al. (2019) |
| Last updated: 2019 | ||||
| ATACProc | Bash; Python; R | Complete pipeline with additional downstream analyses included | ++ | Unpublished Last updated: 2019 |
| Basepair | NA | Commercial. Web-based GUI for complete analysis | ? | Unpublished |
| CIPHER | R; Perl; Python | A data processing platform for ChIP-seq; RNA-seq; MNase-seq; DNase-seq; ATAC-seq; and GRO-seq datasets | + | Guzman & D’Orso (2017) |
| Last updated: 2017 | ||||
| ENCODE | Python; Bash | Complete pipeline following ENCODE standards for ATAC/DNase-seq analysis | ++ | Unpublished |
| Last updated: 2020 | ||||
| esATAC | R | Complete pipeline including downstream analyses | +++ | Wei, Zhang, Fang, Li, & Wang (2018) |
| Last updated: 2019 | ||||
| GUAVA | Java; Python; R | GUI based complete ATAC-seq pipeline | + |
Divate & Cheung (2018) Last updated: 2019 |
| I-ATAC | Java | GUI based interactive ATAC-seq pipeline | + |
Ahmed & Ucar (2017) Last updated: 2017 |
| nfcore/atacseq | Python; R | Complete pipeline build using Nextflow | +++ |
Ewels et al. (2019) Last updated: 2019 |
| PEPATAC | Python; R; Perl | Complete pipeline with unique analytical approaches and QC metrics | +++ | Unpublished Last updated: 2019 |
| pyflow-ATACseq | Bash; Python | ATAC-seq snakemake pipeline with included nucleosome positioning and TF footprinting | ++ | Unpublished |
| Last updated: 2019 | ||||
| snakePipes ATAC-seq | Python | Workflow system including ATAC-seq analysis | +++ |
Bhardwaj et al. (2019) Last updated: 2019 |
| Tobias Rausch | Bash; R; Python | Complete pipeline with emphasis on downstream analyses | ++ |
Rausch et al. (2019)
Last updated: 2020 |