Table 1.

Comparison between GUAVA and available tools for ATAC-seq data analysis.

Features	GUAVA	NucleoATAC	I-ATAC	ATACseqQC	ATAC-Seq/DNase-Seq Pipeline
Graphical user interface	Yes	No	Yes	No	No
Adapter trimming	Yes	No	Yes	No	Yes
Alignment	Yes	No	Yes	No	Yes
Alignment filtering	Yes	No	Yes	No	Yes
Alignment shifting	Yes	Yes	Yes	Yes	Yes
Fragment size distribution plot	Yes	Yes	Yes	Yes	No
Peak calling	Yes	No	Yes	No	Yes
ATAC-seq differential analysis	Yes	No	No	No	No
Visualization of ATAC-seq data tracks	Yes	No	No	Yes	No
Annotation and function analysis	Yes	No	No	No	No
Nucleosome positing	No	Yes	No	Yes	No
Transcription factor foot printing	No	Yes	No	Yes	No

A comparison between GUAVA and currently available tools for ATAC-seq data analysis based on features such read mapping, peak calling, and differential analysis, etc.