Table 1.
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.