Inter-chromosomal translocation identification software tools | Whole-genome sequencing data analysis
Inter-chromosomal translocation is a genetic abnormality cause by rearrangement of parts between nonhomologous chromosomes. Chromosomal translocations play a role in cancer, mainly in leukemia. Software tools are used for genome-wide detection of structural variant and genomic rearrangements from whole-genome sequencing data.
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.
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.
Provides a structural variant caller. TIDDIT detects many different types of structural variants (SVs) such as translocations, inversions, deletions, interspersed duplications, insertions and tandem duplications. It utilizes discordant pairs and split reads to detect the genomic location of structural variants, as well as the read depth information for classification and quality assessment of the variants.