UpPipe: A Novel Pipeline Management on In-Memory Processors for RNA-seq Quantification
RNA sequence quantification is an important analysis method to measure transcript
abundances. A key overhead in RNA-seq quantification is to map a set of RNA reads to …
abundances. A key overhead in RNA-seq quantification is to map a set of RNA reads to …
RNA-seq Quantification on Processing in memory Architecture: Observation and Characterization
In recent years, the processing in memory (PIM) technique has progressively captured
people's attention since it reveals the potential to strike down the von Neumann bottleneck …
people's attention since it reveals the potential to strike down the von Neumann bottleneck …
aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments
A Alonso, BN Lasseigne, K Williams, J Nielsen… - …, 2017 - academic.oup.com
The wide range of RNA-seq applications and their high-computational needs require the
development of pipelines orchestrating the entire workflow and optimizing usage of …
development of pipelines orchestrating the entire workflow and optimizing usage of …
Accelerated genomics data processing using memory-driven computing
Next generation sequencing (NGS) is the driving force behind precision medicine and is
revolutionizing most, if not all, areas of the life sciences. Particularly when targeting the …
revolutionizing most, if not all, areas of the life sciences. Particularly when targeting the …
Holistic optimization of an RNA-seq workflow for multi-threaded environments
For many next generation-sequencing pipelines, the most computationally intensive step is
the alignment of reads to a reference sequence. As a result, alignment software such as the …
the alignment of reads to a reference sequence. As a result, alignment software such as the …
Pim-quantifier: A processing-in-memory platform for mrna quantification
Processing-in-memory (PIM) architecture has been considered as a promising solution for
the “memory-wall” issue in many data-intensive applications, especially in bioinformatics …
the “memory-wall” issue in many data-intensive applications, especially in bioinformatics …
Beacon: Scalable near-data-processing accelerators for genome analysis near memory pool with the cxl support
W Huangfu, KT Malladi, A Chang… - 2022 55th IEEE/ACM …, 2022 - ieeexplore.ieee.org
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment
(eg, COVID-19), and so on. Unfortunately, in genome analysis, the speed of data processing …
(eg, COVID-19), and so on. Unfortunately, in genome analysis, the speed of data processing …
Cram-seq: Accelerating rna-seq abundance quantification using computational ram
RNA Sequence (RNA-Seq) abundance quantification is an important application in different
fields of genomic studies, eg, analysis offunctionally similar genes in a biological sample …
fields of genomic studies, eg, analysis offunctionally similar genes in a biological sample …
Memory-driven computing accelerates genomic data processing
Next generation sequencing (NGS) is the driving force behind precision medicine and is
revolutionizing most, if not all, areas of the life sciences. Particularly when targeting the …
revolutionizing most, if not all, areas of the life sciences. Particularly when targeting the …
A flexible automated pipeline engine for transcript-level quantification from rna-seq
P Cinaglia, M Cannataro - International Conference on Conceptual …, 2022 - Springer
The advances in massive parallel sequencing technologies (ie, Next-Generation
Sequencing) allowed RNA sequencing (RNA-seq). The analysis of RNA-seq data uses a …
Sequencing) allowed RNA sequencing (RNA-seq). The analysis of RNA-seq data uses a …