SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package

BMC Bioinformatics
Taewoon JooHyun Goo Woo

Abstract

Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgently require prompt update of the pipelines. Recent clinical applications of NGS technology such as cell-free DNA, cancer panel, or exosomal RNA sequencing data also require appropriate customization of the processing pipelines. Here, we developed SEQprocess, a highly extendable framework that can provide standard as well as customized pipelines for NGS data processing. SEQprocess was implemented in an R package with fully modularized steps for data processing that can be easily customized. Currently, six pre-customized pipelines are provided that can be easily executed by non-experts such as biomedical scientists, including the National Cancer Institute's (NCI) Genomic Data Commons (GDC) pipelines as well as the popularly used pipelines for variant calling (e.g., GATK) and estimation of allele frequency, RNA abundance (e.g., TopHat2/Cufflink), or DNA copy numbers (e.g., Sequenza). In addition, optimized pipelines for the clinic...Continue Reading

References

May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Oct 30, 2012·Genomics & Informatics·So Mee KwonHyun Goo Woo
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Jan 31, 2015·Nature Methods·Wolfgang HuberMartin Morgan
Feb 3, 2016·BMC Bioinformatics·Patrick Schorderet
Jun 9, 2016·Genome Biology·William McLarenFiona Cunningham
Sep 22, 2016·BMC Bioinformatics·Tyler W H Backman, Thomas Girke

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

VEP
SEQprocess
MuSE
R
BWA
R package
Python
ExpressionSet
Linux
bowtie2

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