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Table 2 A summary of peak calling tools

From: A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

Tool

Algorithm

Approach

Published year

Language

Operating system

Software features

Latest release version

Latest release year

Website

Maintenance

Ref. #

BayesPeak

BayesPeak algorithm

Used Hidden Markov model (HMM) for finding peaks

2011

R and C

Linux, Windows, and Mac OS X

Support multicore

1.12.0

N/A

http://compbio.sysbiol.cam.ac.uk/Resources/BayesPeak/csbayespeak.html

Yes

[54]

BroadPeak

Maximal-segment algorithm, Gibbs sampling algorithm, Ruzzo–Tompa algorithm

Probabilistic model

2013

R

N/A

N/A

One version

2013

http://jordan.biology.gatech.edu/page/software/broadpeak/

Yes

[55]

CisGenome

Two-pass algorithm

Implemented a modular design, use sliding window for peak detection

2008

C, C++

Windows, Mac, and Linux

Stand-alone system, command mode and GUI

v2.0

2011

http://www.biostat.jhsph.edu/~hji/cisgenome/

Yes

[56]

DROMPA (DRaw and observe Multiple enrichment profiles and annotation)

Sliding window

Two-step procedure, DROMPA peak-calling program

2013

ANSI-C

Linux

N/A

1.4.0

2013

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/

Yes

[57]

F-Seq

F-Seq density estimation algorithm

Kernel density estimation

2008

Java

Unix, Linux

N/A

1.84

2011

http://fureylab.web.unc.edu/software/fseq/

Yes

[58]

FindPeaks

Used directional reads module for identifying peaks

Implemented a modular architecture

2008

Java

Linux, Windows, and Mac OS X

Command line

4.0

N/A

http://vancouvershortr.sourceforge.net/

Yes

[59]

GEM (Genome wide Event finding and Motif discovery)

Genome wide event finding and motif discovery (GEM)

Probabilistic model

2012

Java

N/A

Stand-alone software

2.3

2013

http://cgs.csail.mit.edu/gem/

Yes

[60]

GLITR (GLobal Identifier of Target Regions)

GLITR algorithm

Used ChIP-Seq Peak Finder framework

2009

Perl and Python

N/A

N/A

N/A

N/A

N/A

N/A

[61]

GLMNB (Negative binomial generalized linear model)

Sliding window

Generalized Linear Model with Negative binomial distribution

2012

N/A

N/A

N/A

1.0

2012

http://sourceforge.net/projects/glmnb/

N/A

[62]

Hpeak (Hidden Markov model (HMM)-based Peak-finding algorithm)

HMM-based algorithm

Hidden Markov Model (HMM)

2010

Perl and C++

Linux, Windows, and Mac OS

N/A

V2.1

2009

http://www.sph.umich.edu/csg/qin/HPeak/

N/A

[63]

MACS (Model-based analysis of ChIP-Seq)

MACS algorithm (use shift and sliding window algorithm)

Model-based Analysis of ChIP-Seq

2008

Python

Linux

stand-alone, no GUI, open source

1.4.2

2012

http://liulab.dfci.harvard.edu/MACS/

Yes

[64]

NEXT-peak (the normal-exponential two-peak)

NEXT-peak algorithm

Normal-exponential two-peak (NEXT-peak) model

2013

C++

Linux

N/A

1.1

2013

http://ww2.odu.edu/~nxkim/nextpeak/

Yes

[65]

PeakRanger

Same algorithm as PeakSeq for identifying broad regions. Summit-valley-alternator algorithm

Build the read coverage profile

2011

C++

Linux, Mac OS, and Windows

Support parallel cloud computing

1.16

2012

http://ranger.sourceforge.net/

Yes

[66]

PeakSeq

PeakSeq - two-pass strategy

Two-pass strategy

2009

C and Perl

N/A

N/A

1.1

2011

http://info.gersteinlab.org/PeakSeq

N/A

[67]

QuEST (Quantitative Enrichment of Sequence Tags)

Construct profiles and use shifting method

Statistical framework-Kernel Density Estimation approach

2008

C++

Linux, Mac OS

Open source, non-profit use

2.4

2009

http://mendel.stanford.edu/SidowLab/downloads/quest/

No

[68]

SeqSite

Two-step strategy: detect tag-enriched regions and then pinpoint binding sites in the detected regions

Poisson model

2011

C/C++

Windows, Mac OS X, and Linux

Academic use only

1.1.2

2010

http://0-bioinfo-au-tsinghua-edu-cn.brum.beds.ac.uk/software/seqsite/

Yes

[69]

SICER

Scoring scheme

Spatial clustering approach

2009

Python

Linux, Unix

N/A

v1.1

2011

http://home.gwu.edu/~wpeng/Software.htm

Yes

[70]

SIPeS (Site Identification from Paired-end Sequencing)

SIPeS algorithm

Used dynamic fragment pileup value for peak calling

2010

C

Linux

Non-profit use

2.0

2010

http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS

N/A

[71]

SISSRs (Site Identification from Short Sequence Reads)

Site Identification from Short Sequence Reads (SISSRs) algorithm

Sliding window

2008

Perl

Linux, UNIX

N/A

v1.4

2008

http://sissrs.rajajothi.com/

N/A

[72]

Sole-Search

Sole-Search program

Implemented several different analysis steps for peak calling

2010

Java

N/A

Web-based software

N/A

N/A

N/A

No

[73]

T-PIC (Tree shape Peak Identification for ChIP-Seq)

Tree shape Peak Identification for ChIP-Seq (T-PIC) algorithm

Tree-based statistics

2011

R and Perl

N/A

N/A

One version

2011

http://www.math.miami.edu/~vhower/tpic.html

N/A

[74]

USeq

Collection of algorithms and software for peak calling

Implemented several different methods for peak calling

2008

Java

Linux, Mac OS X, and Windows

GUI

8.6.6

2013

http://useq.sourceforge.net/

Yes

[75]

W-ChIPeaks

PELT algorithm and BELT algorithm

Statistical methods control false discovery rate

2011

PHP, Perl, Java and C++

N/A

Web tool

1.0.1

2012

http://motif.bmi.ohio-state.edu/W-ChIPeaks/

Yes for BELT only

[76]

ZINBA (Zero-Inflated Negative Binomial Algorithm)

Zero-Inflated Negative Binomial Algorithm (ZINBA)

Statistical framework

2011

C and R

Mac OS X and Linux/Unix

Support multi-core clusters

2.02.03

2012

http://code.google.com/p/zinba/

Yes

[77]