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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.
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BMC Bioinformatics

ISSN: 1471-2105

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