SeqAssist

BACKGROUND: While 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). RESULTS: SeqAssist 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. CONCLUSIONS: SeqAssist
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.

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

SeqAssist stands for “Sequencing Assistant" and it is a software tool that helps investigators manage next-generation sequencing data by automatically aligning reads to a genome to determine sequence coverage and compare two samples for redundant reads. By utilizing this tool, users can determine the quality of a DNA library for RNA-seq or genome resequencing. 

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