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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics.

Anders Pitman¹, Xiaomeng Huang¹, Gabor T Marth¹

¹UTAH Center for Genetic Discovery, Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, United States.

Bioinformatics (Oxford, England)

|July 27, 2023

Summary

This summary is machine-generated.

Bioinformatics analysis is a bottleneck in precision medicine. The new quickBAM software library accelerates genomic data access, significantly speeding up analysis for faster clinical decisions.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genomic data processing is crucial for precision medicine, but bioinformatics analysis throughput lags behind sequencing capabilities, creating a bottleneck.
Current bioinformatics algorithms do not fully utilize modern hardware, particularly in accessing raw sequencing data from BAM files.
Existing programming libraries for BAM file access fail to leverage parallel input/output capabilities of storage devices.

Purpose of the Study:

To develop a software library that accelerates sequencing data access.
To enable a new generation of high-performance bioinformatics tools.
To address the bottleneck in bioinformatics analysis throughput.

Main Methods:

Developed quickBAM, a software library designed to accelerate sequencing data access.
Exploited the parallelism inherent in commodity storage hardware.
Ported existing analysis software to utilize the quickBAM library.

Main Results:

Analysis software ported to quickBAM demonstrated consistent performance improvements over original versions.
In some cases, analyses completed in under 3 minutes with quickBAM, compared to 1.5 hours with original versions.
quickBAM effectively accelerates sequencing data access, addressing a key bottleneck.

Conclusions:

quickBAM significantly enhances the performance of bioinformatics analysis tools by optimizing data access.
The library enables faster data-informed treatment decisions in time-critical clinical settings like precision medicine.
quickBAM is freely available, promoting the development of next-generation high-performance informatics tools.