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
|