Base quality recalibration software tools | High-throughput sequencing data analysis
Quality score recalibration is trivial if the status of every base (correct or error) is known; the fraction of sequencing errors with a given quality score can be used to calculate the empirical (recalibrated) quality. For real sequencing data, however, erroneous bases are of course not already known. Intriguingly, all current recalibrators are strongly based on this assumption that erroneous bases are known; sequencing errors are identified as mismatches to a reference genome, excluding sites of known variants (e.g., dbSNP for humans). This assumption would be tenable if variant databases were complete, but this is also not the case, and the purpose of sequencing is often to discover variants not present in existing databases. Furthermore, outside of humans and several model organisms, variant databases are not available and thus recalibration is often not done.
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.
Recalibrates base quality scores without assuming knowledge of correct and incorrect bases and without requiring knowledge of common variants. Lacer is an accurate base recalibrator. It enhances variant identification accuracy for resequencing data of human like organisms which improve and extend the benefits of base quality score. Lacer uses an algorithm which directly extracts quality scores and aggregate error probabilities based on the assumption that correct and incorrect bases have different quality score profiles.
Analyzes ancient samples that properly account for post-mortem damage (PMD). ATLAS works directly from raw BAM files and contains all necessary methods to infer patterns of PMD, recalibrate base quality scores and genotype ancient DNA, along with many other tools. The software enables the building of complete and customized pipelines for the analysis of ancient and low-depth samples.