SeQual-Stream: approaching stream processing to quality control of NGS datasets.

ABSTRACT:

Background

Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have the complete genetic dataset before processing can even begin. This limitation clearly hinders quality control performance in those scenarios where the dataset must be downloaded from a remote repository and/or copied to a distributed file system for its parallel processing.

Results

In this paper we present SeQual-Stream, a streaming tool that allows performing multiple quality control operations on genomic datasets in a fast, distributed and scalable way. To do so, our approach relies on the Apache Spark framework and the Hadoop Distributed File System (HDFS)

SUBMITTER: Castellanos-Rodriguez O 

PROVIDER: S-EPMC10612204 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature