Table 1

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

Method

URL

Language

Input

Comments

Ref.


    PEM-based

BreakDancer

http://breakdancer.sourceforge.net webcite/

Perl, C++

Alignment files

Predicting insertions, deletions, inversions, inter- and intra-chromosomal translocations

[17]

PEMer

http://sv.gersteinlab.org/pemer webcite/

Perl, Python

FASTA

Using simulation-based error models to call SVs

[18]

VariationHunter

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

C

DIVETa

Detecting insertions, deletions and inversions

[20]

commonLAW

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

C++

Alignment files

Aligning multiple samples simultaneously to gain accurate SVs using maximum parsimony model

[21]

GASV

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

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 webcite

C++

FASTA

A dynamic-programming algorithm using optimal alignments with gap excision to detect breakpoints

[23]

Pindel

http://www.ebi.ac.uk/~kye/pindel webcite/

C++

BAM /FASTQ

Using a pattern growth approach to identify breakpoints of various SVs

[22]

SLOPE

http://www-genepi.med.utah.edu/suppl/SLOPE webcite

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 webcite/

Python

FASTA

Calling CNV from co-assembled genomes and estimating copy number with Poisson mixture model

[58]

Cortex assembler

http://cortexassembler.sourceforge.net webcite/

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 webcite/

C

SV callsc + BAM

Local assembly of SVs using the iterative graph routing assembly (TIGRA) algorithm

N/A


aThe specific input format for VariationHunter, including the reads with multiple alignments.

bFile format from MAQ mapview.

cThe file including the detected structure variations using other tools.

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

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