Table 4

Combinatorial bioinformatics tools for CNV detection using NGS data

Method

URL

Language

Input

Combinationa

Ref.


NovelSeq

http://compbio.cs.sfu.ca/strvar.htm webcite

C

FASTA/SAM

PEM+AS

[66]

HYDRA

http://code.google.com/p/hydra-sv webcite/

Python

Discordant paired-end mappings

PEM+AS

[67]

CNVer

http://compbio.cs.toronto.edu/CNVer webcite/

Perl, C++

BAM/aligned positions

PEM+RD

[61]

GASVPro

http://code.google.com/p/gasv webcite/

C++

BAM

PEM+RD

[63]

Genome STRiP

http://www.broadinstitute.org/software/genomestrip/genome-strip webcite

Java, R

BAM

PEM+RD

[62]

SVDetect

http://svdetect.sourceforge.net webcite/

Perl

SAM/BAM/ELAND

PEM+RD

[60]

inGAP-sv

http://ingap.sourceforge.net webcite/

Java

SAM

PEM+RD

[64]

SVseq

http://www.engr.uconn.edu/~jiz08001/svseq.html webcite

C

FASTQ/BAM

PEM+SR

[73]

Nord et al.

N/A

N/A

N/A

RD+SR

[74]


aRD: read depth-based approach; PEM: paired-end mapping approach; SR: split read approach; AS: de novo assembly approach.

Zhao et al. BMC Bioinformatics 2013 14(Suppl 11):S1   doi:10.1186/1471-2105-14-S11-S1

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