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 |