Table 1 Usability summary of peak callers.
From: PeakRanger: A cloud-enabled peak caller for ChIP-seq data
| GUI | Command line parameters input | Data format | Customizable input | Automatic format detection | Species | Reusable configuration file | Wiggle file generation | No preprocessing | Parallel processing | Cloud parallel computing | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PeakRanger | Yes | Eland, Bowtie, SAM/BAM, BED | Yes | All | Yes | Yes | Yes | Yes | Yes | ||
| MACS | Yes | Eland, Bowtie, SAM/BAM, BED | Yes | All | Yes | Yes | |||||
| FindPeaks | Yes | Yes | Eland, Bowtie, BED, GFF | All | Yes | ||||||
| SPP | Eland, Bowtie, MAQ, Arachne | All | Yes | Yes | Yes | ||||||
| QuEST | Yes | Eland, Bowtie, Solexa, MAQ | All | Yes | Yes | ||||||
| GPS | Yes | Eland, Bowtie, SAM, NovoAlign, BED | All | Yes | |||||||
| Erange | Yes | Eland, Bowtie, Blat, BED | All | Yes | |||||||
| CisGenome | Yes | Yes | Eland, BED | All | Yes | ||||||
| F-Seq | Yes | BED | All | Yes | Yes | ||||||
| SISSRs | Yes | BED | All | Yes | |||||||
| PeakSeq | Eland | Human | Yes |