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Table 1 Summary of paired-end mapping (PEM), split read (SR), and de novo assembly (AS)-based tools for CNV detection using NGS data

From: Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

Method URL Language Input Comments Ref.
PEM-based      
BreakDancer http://breakdancer.sourceforge.net/ Perl, C++ Alignment files Predicting insertions, deletions, inversions, inter- and intra-chromosomal translocations [17]
PEMer http://sv.gersteinlab.org/pemer/ Perl, Python FASTA Using simulation-based error models to call SVs [18]
VariationHunter http://compbio.cs.sfu.ca/strvar.htm C DIVETa Detecting insertions, deletions and inversions [20]
commonLAW http://compbio.cs.sfu.ca/strvar.htm C++ Alignment files Aligning multiple samples simultaneously to gain accurate SVs using maximum parsimony model [21]
GASV http://code.google.com/p/gasv/ Java BAM A geometric approach for classification and comparison of structural variants [65]
Spanner N/A N/A N/A Using PEM to detect tandem duplications [59]
SR-based      
AGE http://sv.gersteinlab.org/age C++ FASTA A dynamic-programming algorithm using optimal alignments with gap excision to detect breakpoints [23]
Pindel http://www.ebi.ac.uk/~kye/pindel/ C++ BAM /FASTQ Using a pattern growth approach to identify breakpoints of various SVs [22]
SLOPE http://www-genepi.med.utah.edu/suppl/SLOPE C++ SAM/FASTQ/MAQb Locating SVs from targeted sequencing data [26]
SRiC N/A N/A BLAT output CalibratingSV calling using realistic error models [25]
AS-based      
Magnolya http://sourceforge.net/projects/magnolya/ Python FASTA Calling CNV from co-assembled genomes and estimating copy number with Poisson mixture model [58]
Cortex assembler http://cortexassembler.sourceforge.net/ C FASTQ/FASTA Using alignment of de novo assembled genome to build de Bruijn graph to detect SVs [57]
TIGRA-SV http://gmt.genome.wustl.edu/tigra-sv/ C SV callsc + BAM Local assembly of SVs using the iterative graph routing assembly (TIGRA) algorithm N/A
  1. aThe specific input format for VariationHunter, including the reads with multiple alignments.
  2. bFile format from MAQ mapview.
  3. cThe file including the detected structure variations using other tools.
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