A software package for efficient patient trajectory analysis applied to analyzing bladder cancer development.

We present the Patient Trajectory Analysis Library (PTRA), a software package for explorative analysis of patient development. PTRA provides the tools for extracting statistically relevant trajectories from the medical event histories of a patient population. These trajectories can additionally be clustered for visual inspection and identifying key events in patient progression.

Halvade somatic: Somatic variant calling with Apache Spark.

Background: The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements.

Multithreaded variant calling in elPrep 5.

We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps.

Comparing Ease of Programming in C++, Go, and Java for Implementing a Next-Generation Sequencing Tool.

elPrep is an extensible multithreaded software framework for efficiently processing Sequence Alignment/Map (SAM)/Binary Alignment/Map (BAM) files in next-generation sequencing pipelines. Similar to other SAM/BAM tools, a key challenge in elPrep is memory management, as such programs need to manipulate large amounts of data. We therefore investigated 3 programming languages with support for assisted or automated memory management for implementing elPrep, namely C++, Go, and Java.

A comparison of three programming languages for a full-fledged next-generation sequencing tool.

Background: elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other SAM/BAM tools, management of heap memory is a complex task in elPrep, and it became a serious productivity bottleneck in its original implementation language during recent further development of elPrep.

elPrep 4: A multithreaded framework for sequence analysis.

We present elPrep 4, a reimplementation from scratch of the elPrep framework for processing sequence alignment map files in the Go programming language. elPrep 4 includes multiple new features allowing us to process all of the preparation steps defined by the GATK Best Practice pipelines for variant calling. This includes new and improved functionality for sorting, (optical) duplicate marking, base quality score recalibration, BED and VCF parsing, and various filtering options.

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce.

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets.

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.

elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline.

Halvade: scalable sequence analysis with MapReduce.

Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine.

Results: We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner.