Table 1 Parameters implemented in SEQprocess

None

fastq.dir

Fastq file path

File path

output.dir

Output directory

File path

config.fn

Configure file path

File path

project.name

Project name

Name

type

Data type

WGS, WES, BarSEQ, RSEQ, miRSEQ

pipeline

Select data processing pipeline

none, GDC, GATK, BarSEQ, Tuxedo, miRSEQ

mc.cores

Number of multi core

Numeric

run.cmd

Whether to execute the command line

Logical

QC

QC

Quality Check (FastQC)

Logical

Trimming

trim.method

Trimming (Cutadapt, TrimGalore)

trim.galore, cutadapt, none

Alignment

align.method

Alignment (BWA, Tophat2, STAR, Bowtie2)

bwa, tophat2, star, bowtie2, none

build.transcriptome.idx

Transcriptome criterion generation in tophat

Logical

tophat.thread.number

Number of threads

Numeric

bwa.method

Select BWA method

mem, aln

bwa.thread.number

Number of threads

Numeric

star.thread.number

Number of threads

Numeric

Remove Duplicates

rm.dup

Whether to execute Picard MarkDuplicates

MarkDuplicates, BARCODE, none

Re-alignment

realign

Whether Re-alignment

Logical

Variant Call

variant.call.method

Select variant calling method

gatk, varscan2, mutect2, muse, somaticsniper, none

gatk.thread.number

Number of threads

Numeric

mut.cnt.cutoff

Read depth criterion determining the presence or absence of mutation

Numeric

Annotation

annotation.method

Select variant annotation method

annovar, vep

ref

Reference version

Default = hg38

RNA quantitation

rseq.abundance.method

Select RNA quantitation method

cufflinks, htseq, none

cufflinks.gtf

Whether detection novel genes and isoforms

-G, −g

cufflinks.thread.number

Number of threads

Numeric

RNAtype

Type of RNA

mRNA, miRNA

DNA copy number

CNV

Whether quantitation CNV

Logical

ExpressionSet/SE

R object

make.eSet

Make ExpressionSet Rdata

Logical

eset2SummarizedExperiment

Convert eSet to SE

Logical

Report

report.mode

Creating report file

Logical