Indel realignment software tools | High-throughput sequencing data analysis
Despite the fact that both Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) have been widely used in biological studies and rare disease diagnosis, limitations of these techniques on insertion and deletion (INDEL calling are still not well characterized. INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.
Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and able to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
Allows next-generation sequencing read alignments. ABRA’s algorithm performs localized region assembly, contig building, alignment of assembled contigs and read realignment. The software identifies variations that are not present in the original read alignments and improves allele-frequency estimates for variations that are present. It can be used to enhance both germ-line and somatic variant detection and works with paired-end as well as single-end data.
Performs genomic data analysis. HiGene is a platform aiming to assist in the computation of resource allocation and skew processing of genomic data analysis. This software exploits Apache Spark to parallelize the GATK pipeline and improves pipeline performance by a combined optimization of resource usage at fine-grained level with the resolving of the task skew problem from both data and computation aspects. It was evaluated on a whole genome sequencing (WGS) dataset.
Performs a complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results. A user can perform the whole analysis without knowing the underlying hardware and software architecture, dealing with both paired and single end data. The interface provides an easy and intuitive access for data submission and user-friendly web pages for annotated variant visualization.
Contains features for studying whole genome sequencing (WGS) and whole exome sequencing (WES) data. DNAp is a program able to detect mutations from diseases samples and can be applied to work on human and mouse samples. For performing, this tool requires that users provide several information such as the word “tumor”, or the word “normal”.
Discovers large indels using optical maps (OM) reads with weak signal. OMIndel consists of an alignment-based method combined with local assembly-like approach. It records information of the discordance, including for instance the coordinates on the reference and sizing difference. This tool creates a graph for the discordant records and a graph-based union-find algorithm for retrieving all connected components of this graph.
Discovers complex mobile element insertion (MEI) signals. rMETL extracts chimeric reads and deduces a set of infers putative MEI sites. It uses a set of specifically designed rules for clustering the chimerically aligned read parts. This tool can study the realignment results to retrieve the evidences to call MEIs as well as filter false positive candidates. It is useful for transforming the ambiguous and chimeric read alignments into more homogenous alignments.