Table 1.
Pipelines for bulk ATAC-seq data analysis
| Name | Data type | Input format | Function | Advantages | Download website | Language | Platform |
|---|---|---|---|---|---|---|---|
| ALTRE [80] | ATAC-seq | CSV BAM BED |
(i) Peak merging and annotation, (ii) differential analysis, (iii) pathway enrichment analysis | (i) Easy-to-use (ii) Allows for parameters change (iii) A shiny website platform |
https://github.com/Mathelab/ALTRE | R | Windows, Linux, MacOS |
| ATAC-pipe [84] | ATAC-seq | FASTQ | (i) QC, (ii) alignment, (iii) peak calling, (iv) differential analysis, (v) search for motifs, (vi) TF footprinting, (vii) Regulatory network reconstruction | (i) Integrated pipeline with multiple toolkits (ii) High-quality figures |
https://github.com/QuKunLab/ATAC-pipe | Python | Linux, MacOS |
| atacR [81] | ATAC-seq | BAM CSV |
(i) Normalization, (ii) differential analysis | (i) Allows for normalization (ii) Diagnostic plots |
https://github.com/TeamMacLean/atacr | R | Platform independent |
| Ataqv [78] | ATAC-seq | BAM | (i) QC with visualization | (i) Diverse QC metrics (ii) Quick and convenient visualization |
https://github.com/ParkerLab/ataqv/ | C++ | Linux, MacOS |
| CIPHER [88] | ATAC-seq ChIP-seq RNA-seq MNase-seq DNase-seq GRO-seq |
FASTQ | (i) QC, (ii) alignment, (iii) peak calling, (iv) peak annotation and visualization, (v) differential analysis, (vi) motif identification | (i) Stand-alone workflow platform (ii) Integrates multiple NGS data (iii) Extensive and detailed QC reports |
https://github.com/c-guzman/cipher-workflow-platform | Nextflow, R | Linux, MacOS |
| COCOA [95] | ATAC-seq DNA methylation data |
Counts matrix | (i) quantify inter-sample variation (ii) annotating variations |
(i) Supports supervised and unsupervised analysis (ii) Integrated with multi-omics analyses |
http://bioconductor.org/packages/COCOA | R | Windows, MacOS |
| DEBrowser [86] | ATAC-seq RNA-seq |
Counts matrix | (i) QC, (ii) differential analysis, (iii) pathway analysis | (i) A shiny website platform (ii) Interactive analysis (iii) Diverse plots |
https://bioconductor.org/packages/release/bioc/html/debrowser.html | R | Platform independent |
| diffTF [96] | ATAC-seq ChIP-seq RNA-seq |
BAM BED |
(i) calculate differential TF activity, (ii) classify TF with RNA-seq data | Classify TF into activators or repressors | https://git.embl.de/grp-zaugg/diffTF | Snakemake | Cluster system |
| esATAC [82] | ATAC-seq | FASTQ | (i) QC, (ii) alignment, (iii) peak calling, (iv) peak annotation, (v) motif analysis | (i) Perform ‘one command line for results’ analysis (ii) Maximize memory control and parallel computing |
https://www.bioconductor.org/packages/release/bioc/html/esATAC.html | R and C++ | Windows, Linux, MacOS |
| GUAVA [89] | ATAC-seq | FASTQ | (i) QC, (ii) alignment, (iii) peak calling, (iv) peak annotation, (v) differential analysis, (vi) functional annotation | (i) Standalone software (ii) Diverse plots |
https://github.com/MayurDivate/GUAVA | JAVA | Linux, MacOS |
| I-ATAC [83] | ATAC-seq ChIP-seq WGS-seq |
FASTQ | (i) QC, (ii) alignment, (iii) peak calling | (i) Standalone software (ii) Easy-to-use (iii) One-click operation |
https://github.com/UcarLab/I-ATAC | JAVA | UNIX, Linux, Windows, MacOS |
| MMARGE [79] | ATAC-seq ChIP-seq DNase-seq |
FASTQ VCF |
(i) alignment, (ii) TF and motif analysis | Identify combinations of TFs | https://github.com/vlink/marge | Perl and R | UNIX |
| Octopus-toolkit [90] | ATAC-seq ChlP-seq DNase-seq MeDIP-seq MNase-seq RNA-seq |
SRA FASTQ |
(i) QC, (ii) alignment, (iii) peak calling, (iv) peak annotation, (v) motif analysis | (i) Standalone software (ii) Retrieving SRA files from the GEO database (iii) Provides several model genomes (iv) Allows meta-analysis |
https://github.com/kangk1204/Octopustoolkit2 | JAVA | Linux, MacOS |
| Recoup [85] | ATAC-seq ChIP-seq RNA-seq |
BAM BED BIGWIG |
(i) Signal normalization , (ii) coverage profile analysis | (i) High-quality figures (ii) Fast and quick output |
https://bioconductor.org/packages/recoup | R | Linux, Windows, MacOS |
| snakePipes [87] | ATAC-seq ChIP-seq RNA-seq Bisulfite-seq Hi-C RNA-seq |
FASTQ BAM |
(i) QC, (ii) alignment, (iii) peak calling, (iv) differential analysis | (i) Integrates multiple NGS data, (ii) Extensive and detailed QC reports (iii) Allows for parameters change |
https://github.com/maxplanck-ie/snakepipes | Snakemake | Cluster system |
| TOBIAS [97] | ATAC-seq | BAM FASTA PWM |
(i) Bias correction, (ii) footprint analysis, (iii) differential analysis | (i) Focus on footprint analysis (ii) Time-series data analysis (iii) Data visualization within one framework |
https://github.com/loosolab/TOBIAS | Python | Cluster system |