Deletion identification software tools | High-throughput sequencing data analysis
Advances of next generation sequencing technologies and availability of short read data enable the detection of structural variations (SVs). Deletions, an important type of SVs, have been suggested in association with genetic diseases. There are three types of deletions: blunt deletions, deletions with microhomologies and deletions with microsinsertions. The last two types are very common in the human genome, but they pose difficulty for the detection. Furthermore, finding deletions from sequencing data remains challenging.
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 computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. breseq reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.
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.
Affords a way for analysis of Pacific Biosciences long-read sequencing data. PBSuite is composed of two projects: PBJelly and PBHoney. The first one is an automated pipeline for aligning long sequencing reads to draft assembles. The second provides identification approaches for analyze high mappability of long reads considering intra red discordance and soft-clipped tails.
Allows structural variant (SV) discovery. LUMPY is a general probabilistic SV discovery framework that integrates multiple SV detection signals, including those generated from read alignments or prior evidence. The software is based upon a general probabilistic representation of an SV breakpoint that allows any number of alignment signals to be integrated into a single discovery process. It can detect SV from multiple alignment signals in files from one or more samples. A simplified wrapper for standard analyses, LUMPY Express, can also be executed.
Retrieves balanced and unbalanced forms of structural variation, such as deletions, tandem duplications, inversions and translocations. DELLY is based on a combination of short-range and long-range paired-end mapping and split-read analysis. It is useful for massively parallel sequencing (MPS) data from various sources, including deep whole-genome sequencing data and low-pass mate-pair sequencing data with longer inserts.