Quality assessment software tools | Whole-exome sequencing data analysis
Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human genome. The efficiency and the lack of bias in the enrichment process need to be assessed as a quality control step before performing downstream analysis of the sequence data. Tools that can report on the sensitivity, specificity, uniformity and other enrichment-specific features are needed.
Targets enrichment performance for next-generation sequencing (NGS). NGSrich meets the demand for a detailed, summarized, and exon-wise analysis of the target enrichment performance of NGS libraries. The software was developed as a part of a computational pipeline used for high-throughput analysis of target-enriched resequencing experiments.
Provides quality assessment of target enrichment experiments. TEQC enables users to leverage a multitude of methods to monitor the target enrichment process. Moreover, TEQC allows to evaluate the amount of read duplication and its effect on target coverage, as well as the relation between GC content of the capture hybridization probes and coverage for the respective bases. It imports genomic positions of sequencing reads and target regions, and allows to evaluate the whole enrichment process by estimating specificity and sensitivity of the capture, per-target read coverage and amount of read duplication.
Enables tightly integrated comparative variant analysis and visualization of thousands of next generation sequencing (NGS) data samples and millions of variants. BasePlayer is a highly efficient and user-friendly software for biological discovery in large-scale NGS data. It transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.
Allows detection of sequencing problems limiting sequence read length. QualTrace is a DNA sequencing quality control (QC) analysis program that analyzes trace files collected on the ABI 3730 and 3730xl DNA sequencers. The software can detect nine common sequencing sample problems that limit the read length of sequenced DNA. It can be integrated into sequencing data pipeline and bioinformatics infrastructure. A graphical version, called Auto QualTrace, designed for small to medium sized DNA sequencing facilities is also available.
Offers a platform for multiplex data analysis. MILLIPLEX is an interface intending to automate the detection of features related to the investigated data. It provides multiple quality control values, can handle values for CHI and CV, including from the analysis of large datasets. This application is compatible with data derived from software such as Bio-Plex, Miraibio, and broadly with data from the Luminex xPONENT system.