Detects breakpoints of large deletions and medium sized insertions from paired-end short reads. Pindel is a program that uses pattern growth algorithm to identify the break points of large deletions (1 bp–10 kb) and medium sized insertions (1–20 bp) from 36 bp paired-end short reads. The software can be useful for addressing the structural variations between individuals from next-gen high throughput sequencing.
A tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture 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.
Provides computational tools and methods for high-quality insertion sequence (IS) annotation. ISsaga uses established ISfinder annotation standards and permits rapid processing of single or multiple prokaryote genomes. ISsaga provides general prediction and annotation tools, information on genome context of individual ISs and a graphical overview of IS distribution around the genome of interest.
Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping quality and associated tandem repeat, are used to evaluate the quality of predicted structural variation. Compared with other approaches, it can detect many more large insertions and complex variants with lower false discovery rate. Moreover, inGAP-sv, written in Java programming language, provides a user-friendly interface and can be performed in multiple operating systems.
Identifies genomic structural variations from paired-end and mate-pair sequencing data. SVDetect isolates and predicts intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing furnished by the high-throughput sequencing technologies. This software proceeds first by collecting all pairs that are suspected to come from the same structural variant (SV). It then employs a sliding-window strategy to detect all groups of pairs sharing similar genomic location.
A comprehensive analysis platform for the processing, analysis and visualization of structural variation based on sequencing data or genomic microarrays, enabling the rapid identification of disease loci or genes. Vivar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe but still easy to share, and is easy expandable as analysis techniques advance.