Skip to main content

Advertisement

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.
Back to article page