Comparison of high-throughput sequencing data compression tools.

High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a reference, in SAM format, both with large memory footprints. Worldwide growth of HTS data has prompted the development of compression methods that aim to significantly reduce HTS data size. Here we report on a benchmarking study of available compression methods on a comprehensive set of HTS data using an automated framework.

Toward a common standard for data and specimen provenance in life sciences.

Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.

An Implantable Wireless System for Remote Hemodynamic Monitoring of Heart Failure Patients.

This article presents an implantable wireless system for remote hemodynamic monitoring, which enables direct, continuous (24/7), and simultaneous measurement of pulmonary arterial pressure (PAP) and cross-sectional area (CSA) of the artery. The implantable device, which measures 3.2 mm × 2 mm × 10 mm, comprises a piezoresistive pressure sensor, an ASIC implemented in 180-nm CMOS, a piezoelectric ultrasound (US) transducer, and a nitinol anchoring loop. An energy-efficient pressure monitoring system, which employs duty-cycling and spinning excitation technique, achieves 0.44 mmHg resolution in a pressure range from -135 mmHg to +135 mmHg and consumes 1.1 nJ conversion energy. The artery diameter monitoring system utilizes the inductive characteristic of the implant's anchoring loop and achieves 0.24 mm resolution within a diameter range of 20 mm to 30 mm, four times higher than echocardiography lateral resolution. The wireless US power and data platform enables simultaneous power and data transfer employing a single piezoelectric transducer in the implant. The system is characterized with an 8.5 cm tissue phantom and achieves a US link efficiency of 1.8%. The uplink data is transmitted by using an ASK modulation scheme parallel to the power transfer and achieves a modulation index of 26%. The implantable system is tested in an in-vitro experimental setup, which emulates the arterial blood flow, and accurately detects fast pressure peaks for systolic and diastolic pressure changes at both 1.28 MHz and 1.6 MHz US powering frequencies, with corresponding uplink data rates of 40 kbps and 50 kbps.

An Energy-Efficient Bridge-to-Digital Converter for Implantable Pressure Monitoring Systems.

This paper presents an energy-efficient, duty-cycled, and spinning excitation bridge-to-digital converter (BDC) designed for implantable pressure sensing systems. The circuit provides the measure of the pulmonary artery pressure that is particularly relevant for the monitoring of heart failure and pulmonary hypertension patients. The BDC is made of a piezoresistive pressure sensor and a readout integrated circuit (IC) that comprises an instrumentation amplifier (IA) followed by an analog-to-digital converter (ADC). The proposed design spins both the bridge excitation and the ADC's sampling input voltages simultaneously and exploits duty cycling to reduce the static power consumption of the bridge sensor and IA while cancelling the IA's offset and 1/f noise at the same time. The readout IC has been designed and fabricated in a standard 180-nm CMOS process and achieves 8.4 effective number of bits (ENOB) at 1 kHz sampling rate while drawing 0.53 µA current from a 1.2 V supply. The BDC, built with the readout IC and a differential pressure sensor having 5 k Ω bridge resistances, achieves 0.44 mmHg resolution in a 270 mmHg pressure range at 1 ms conversion time. The current consumption of the bridge sensor by employing duty cycling is reduced by 99.8% thus becoming 0.39 µA from a 1.2 V supply. The total conversion energy of the pressure sensing system is 1.1 nJ, and achieves a figure-of-merit (FoM) of 3.3 pJ/conversion, which both represent the state of the art.

Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment.

The intrinsic high-entropy sequence metadata, known as quality scores, is largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collateral side effects. In this article, we leverage on the penalty functions of HISAT2 aligner to rebin the quality score scale in such a way as to avoid any impact on sequence alignment, identifying alongside a distortion threshold for "safe" quality score representation. We tested our findings on whole-genome and RNA-seq data, and contrasted the results with three methods for lossy compression of the quality scores.

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

This paper provides the specification and an initial validation of an evaluation framework for the comparison of lossy compressors of genome sequencing quality values. The goal is to define reference data, test sets, tools and metrics that shall be used to evaluate the impact of lossy compression of quality values on human genome variant calling. The functionality of the framework is validated referring to two state-of-the-art genomic compressors. This work has been spurred by the current activity within the ISO/IEC SC29/WG11 technical committee (a.k.a. MPEG), which is investigating the possibility of starting a standardization activity for genomic information representation.