SPR detailed installation instructions

systemPipeR Installation

To install the systemPipeR package (H Backman and Girke 2016), please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

To obtain the most recent updates immediately, one can install it directly from GitHub as follow:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("tgirke/systemPipeR", dependencies = TRUE)

Third-party software tools in SPR

Current, systemPipeR provides the param file templates for third-party software tools. Please check the listed software tools.

Tool NameDescriptionStep
bwaBWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. Alignment
Bowtie2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.Alignment
FASTX-ToolkitFASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.Read Preprocessing
TransRateTransrate is software for de-novo transcriptome assembly quality analysis.Quality
GsnapGSNAP is a genomic short-read nucleotide alignment program.Alignment
SamtoolsSamtools is a suite of programs for interacting with high-throughput sequencing data.Post-processing
TrimmomaticTrimmomatic is a flexible read trimming tool for Illumina NGS data.Read Preprocessing
RsubreadRsubread is a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads.Alignment
PicardPicard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.Manipulating HTS data
BuscoBUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.Quality
Hisat2HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) to reference genomes.Alignment
Tophat2TopHat is a fast splice junction mapper for RNA-Seq reads.Alignment
GATKVariant Discovery in High-Throughput Sequencing Data.Variant Discovery
STARSTAR is an ultrafast universal RNA-seq aligner.Alignment
Trim_galoreTrim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files.Read Preprocessing
TransDecoderTransDecoder identifies candidate coding regions within transcript sequences.Find Coding Regions
TrinityTrinity assembles transcript sequences from Illumina RNA-Seq data.denovo Transcriptome Assembly
TrinotateTrinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes.Transcriptome Functional Annotation
MACS2MACS2 identifies transcription factor binding sites in ChIP-seq data.Peak calling
Kallistokallisto is a program for quantifying abundances of transcripts from RNA-Seq data.Read counting
BCFtoolsBCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.Variant Discovery
BismarkBismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.Bisulfite mapping
FastqcFastQC is a quality control tool for high throughput sequence data.Quality
BlastBLAST finds regions of similarity between biological sequences.Blast


H Backman, Tyler W, and Thomas Girke. 2016. “systemPipeR: NGS workflow and report generation environment.” BMC Bioinformatics 17 (1): 388. https://doi.org/10.1186/s12859-016-1241-0.

Last modified 2023-10-02 : rebuild no_render (acf0bd05)