MOTIVATION: Next-Generation Sequencing has led to the availability of massive genomic datasets whose processing raises many challenges, including the handling of sequencing errors. This is especially pertinent in cancer genomics, e.g. for detecting low allele frequency variations from circulating tumor DNA. Barcode tagging of DNA molecules with unique molecular identifiers (UMI) attempts to mitigate sequencing errors; UMI tagged molecules are polymerase chain reaction (PCR) amplified, and the PCR copies of UMI tagged molecules are sequenced independently. However, the PCR and sequencing steps can generate errors in the sequenced reads that can be located in the barcode and/or the DNA sequence. Analyzing UMI tagged sequencing data requires an initial clustering step, with the aim of grouping reads sequenced from PCR duplicates of the same UMI tagged molecule into a single cluster, and the size of the current datasets requires this clustering process to be resource-efficient. RESULTS: We introduce Calib, a computational tool that clusters paired-end reads from UMI tagged sequencing experiments generated by substitution-error-dominant sequencing platforms such as Illumina. Calib clusters are defined as connected components of a graph whose edges are defined in terms of both barcode similarity and read sequence similarity. The graph is constructed efficiently using locality sensitive hashing and MinHashing techniques. Calib's default clustering parameters are optimized empirically, for different UMI and read lengths, using a simulation module that is packaged with Calib. Compared to other tools, Calib has the best accuracy on simulated data, while maintaining reasonable runtime and memory footprint. On a real dataset, Calib runs with far less resources than alignment-based methods, and its clusters reduce the number of tentative false positive in downstream variation calling. AVAILABILITY AND IMPLEMENTATION: Calib is implemented in C++ and its simulation module is implemented in Python. Calib is available at https://github.com/vpc-ccg/calib. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Progress bars are prevalent in modern user interfaces. Typically, a linear function is employed such that the progress of the bar is directly proportional to how much work has been completed. However, numerous factors cause progress bars to proceed at non-linear rates. Additionally, humans perceive time in a non-linear way. This paper explores the impact of various progress bar behaviors on user perception of process duration. The results are used to suggest several design considerations that can make progress bars appear faster and ultimately improve users' computing experience.

Empirical performance evaluation of parallel systems and applications can generate significant amounts of performance data and analysis results from multiple experiments as performance is investigated and problems diagnosed. Hence, the management of performance information is a core component of performance analysis tools. To better support tool integration, portability; and reuse, there is a strong motivation to develop performance data management technology that can provide a common foundation for performance data storage, access, merging, and analysis. This paper presents the design and implementation of the performance data management framework (PerfDMF). PerfDMF addresses objectives of performance tool integration, interoperation, and reuse by providing common data storage, access, and analysis infrastructure for parallel performance profiles. PerfDMF includes an extensible parallel profile data schema and relational database schema, a profile query and analysis programming interface, and an extendible toolkit for profile import/export and standard analysis. We describe the PerfDMF objectives and architecture, give detailed explanation of the major components, and show examples of PerfDMF application.