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Table 1 Parameters implemented in SEQprocess

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

Analysis Steps Parameters Description Values
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