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Table 4 Combinatorial bioinformatics 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 Combinationa Ref.
NovelSeq http://compbio.cs.sfu.ca/strvar.htm C FASTA/SAM PEM+AS [66]
HYDRA http://code.google.com/p/hydra-sv/ Python Discordant paired-end mappings PEM+AS [67]
CNVer http://compbio.cs.toronto.edu/CNVer/ Perl, C++ BAM/aligned positions PEM+RD [61]
GASVPro http://code.google.com/p/gasv/ C++ BAM PEM+RD [63]
Genome STRiP http://www.broadinstitute.org/software/genomestrip/genome-strip Java, R BAM PEM+RD [62]
SVDetect http://svdetect.sourceforge.net/ Perl SAM/BAM/ELAND PEM+RD [60]
inGAP-sv http://ingap.sourceforge.net/ Java SAM PEM+RD [64]
SVseq http://www.engr.uconn.edu/~jiz08001/svseq.html C FASTQ/BAM PEM+SR [73]
Nord et al. N/A N/A N/A RD+SR [74]
  1. aRD: read depth-based approach; PEM: paired-end mapping approach; SR: split read approach; AS: de novo assembly approach.