A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.
Finds genomic rearrangements, including translocations, inversions and deletions. FACTERA can perform with high specificity without compromising sensitivity. It is able to define fusion genes and breakpoints in targeted sequencing data. This tool is applicable on paired-end and soft-clipped reads and is useful for whole genome shotgun sequencing investigation. It aligns all soft-clipped and unmapped reads against each candidate fusion sequence.
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants.
An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes.
Quantifies evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of a structural variation by (i) the number of its soft-clipped bases and (ii) the quality of its alignment to the junction. SV-STAT is more accurate than alternative methods for determining base-pair resolved breakpoints. SV-STAT is a significant advance towards accurate detection and genotyping of genomic rearrangements from DNA sequencing data.
A tool to generate local assemblies of breakpoints genome-wide. NovoBreak is an algorithm used in cancer genomic studies to discover structural variants (both somatic and germline) breakpoints in whole-genome sequencing data. Assemblies realized by novoBreak are based on clusters of reads which share a set of short nucleotide stretches of length K (K-mers) present in a subject genome but not in the reference genome or control data.