SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data

BMC Bioinformatics

Proceedings

Natalie D Barker¹  Ping Gong¹  Alan J Kennedy²  Jennifer G Laird²  Yan Peng³  Andrew S Maxwell³  Nan Wang³  Chaoyang Zhang³ 

[1] Badger Technical Services, LLC, 78216, San Antonio, TX, USA;Environmental Laboratory, U.S. Army Engineer Research and Development Center, 39180, Vicksburg, MS, USA;School of Computing, University of Southern Mississippi, 39406, Hattiesburg, MS, USA;

关键词: SeqAssist;    next generation sequencing (NGS);    sequencing data analysis;    genome-wide coverage;    breadth;    depth;    evenness;    genome (re-)sequencing;    RNA-Seq;    FASTQ;    BWA-MEM.;   

DOI  :  10.1186/1471-2105-15-S11-S10

来源: Springer

【 摘 要 】

BackgroundWhile next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an effort to fill this gap to keep up with the fast pace of technological advancement and to accelerate data-to-results turnaround, we developed a novel software package named SeqAssist ("Sequencing Assistant" or SA).ResultsSeqAssist takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. It consists of three separate workflows: (1) the SA_RunStats workflow generates basic statistics about an NGS dataset, including numbers of raw, cleaned, redundant and unique reads, redundancy rate, and a list of unique sequences with length and read count; (2) the SA_Run2Ref workflow estimates the breadth, depth and evenness of genome-wide coverage of the NGS dataset at a nucleotide resolution; and (3) the SA_Run2Run workflow compares two NGS datasets to determine the redundancy (overlapping rate) between the two NGS runs. Statistics produced by SeqAssist or derived from SeqAssist output files are designed to inform the user: whether, what percentage, how many times and how evenly a genomic locus (i.e., gene, scaffold, chromosome or genome) is covered by sequencing reads, how redundant the sequencing reads are in a single run or between two runs. These statistics can guide the user in evaluating the quality of a DNA library prepared for RNA-Seq or genome (re-)sequencing and in deciding the number of sequencing runs required for the library. We have tested SeqAssist using a synthetic dataset and demonstrated its main features using multiple NGS datasets generated from genome re-sequencing experiments.ConclusionsSeqAssist is a useful and informative tool that can serve as a valuable "assistant" to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments.

【 授权许可】

Unknown   
© Peng et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.