Computational Systems Biology Methods and Protocols.7z

SeqMaker is a tool which generates sequencing reads with SNV,

INDEL, CNV, and gene fusion enabled, with sequencing error and

PCR bias integrated. This tool uses a JSON format profile file to

describe the sequencing simulation settings, and a BED format like

TSV file to configure the target regions of capturing. First, the

simulator samples DNA fragments from whole genome or the

target regions configured by the panel file, and CNVs are simulated

in this process. Second, the DNA fragments will be altered to

simulate SNVs, INDELs, and gene fusions according to the varia-

tion list configured in the profile file. Third, a sequencing process

will be simulated on each DNA fragment to generate NGS reads,

and sequencing errors and amplification bias are also simulated in

this process. Finally, generated reads are written into FASTQ files.

SeqMaker is written in Julia, and the source code is available at

GitHub:https://github.com/OpenGene/SeqMaker.jl. Currently,

it only supports Illumina platforms. More efforts are needed to

build simulators for other platforms, especially the new generations

of sequencers like PacBio and Nanopore platforms.

3 Discussion

As an innovative method in cancer field, liquid biopsy has current or

potential applications in cancer diagnosis, monitoring, and screen-

ing. Cell-free tumor DNA, as a major component of liquid biopsy,

has been widely used in personalized drug guidance for tumor

patients. For those patients not suitable for taking tissue samples

by surgery or needle puncture, ctDNA sequencing gives them new

opportunities for diagnosis of tumors.

Table 5
A comparison of SeqMaker and other NGS simulators

SNV INDEL INV TRA CNV UMI

SeqMaker Yes Yes Yes Yes Yes Yes

BEAR No No No No No No

dwgsim Yes Yes Yes Yes No No

GemSIM Yes No No No No No

Grinder Yes Yes No No No No

Mason Yes Yes No No No No

pIRS Yes Yes Yes No No No

SInC Yes Yes No No Yes No

wgsim Yes Yes No No No No

90 Shifu Chen et al.