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 Name Description Step
bwa BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.  Alignment
Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Alignment
FASTX-Toolkit FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Read Preprocessing
TransRate Transrate is software for de-novo transcriptome assembly quality analysis. Quality
Gsnap GSNAP is a genomic short-read nucleotide alignment program. Alignment
Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. Post-processing
Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. Read Preprocessing
Rsubread Rsubread is a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads. Alignment
Picard Picard 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
Busco BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs. Quality
Hisat2 HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) to reference genomes. Alignment
Tophat2 TopHat is a fast splice junction mapper for RNA-Seq reads. Alignment
GATK Variant Discovery in High-Throughput Sequencing Data. Variant Discovery
STAR STAR is an ultrafast universal RNA-seq aligner. Alignment
Trim_galore Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files. Read Preprocessing
TransDecoder TransDecoder identifies candidate coding regions within transcript sequences. Find Coding Regions
Trinity Trinity assembles transcript sequences from Illumina RNA-Seq data. denovo Transcriptome Assembly
Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes. Transcriptome Functional Annotation
MACS2 MACS2 identifies transcription factor binding sites in ChIP-seq data. Peak calling
Kallisto kallisto is a program for quantifying abundances of transcripts from RNA-Seq data. Read counting
BCFtools BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. Variant Discovery
Bismark Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. Bisulfite mapping
Fastqc FastQC is a quality control tool for high throughput sequence data. Quality
Blast BLAST 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.