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Table 2 External programs and data files used in SEQprocess

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

Pipeline Required R package Programs path Reference path
No matter parallel   
Report Limma, data.table,
fastqcr, pander, knitr, png, grid, gridExtra, ggplot2, reshape2
  
QC   fastqc.dir  
Trimming . trim_galore.path
cutadapt.path
 
Alignment . bwa.path
tophat2.path
bowtie2.path
STAR.path
samtools.path
ref.fa
chrom.fa
bwa.idx
bowtie.idx
star.idx.dir
transcriptome.idx
Remove Duplicates . picard.path ref.fa
chrom.fa
Re-alignment . GATK.path ref.fa
ref.gold_indel
Variant Call   varscan.path
MuSE.path
somaticsniper.path
ref.gold_indel
ref.dbSNP
cosmic.vcf
Annotation . vep.path
vcf2annovar.pl
table_annovar.pl
annovar.db.dir
vep.dir
RNA quantitation GenomicRanges cufflinks.path
htseq.path
ref.gtf
mir.gff
refGene.path
DNA copy number sequenza sequenza.util ref.fa
ExpressionSet/SE
R object
Biobase, GenomicRanges,
SummarizedExperiment