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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]