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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    
  1. This table summarizes commonly supported software features by existing peak callers.