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")
BiocManager::install("systemPipeR")
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 |
References
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 2021-12-06: update plotwf; no_render; pg_build (1cae34aa)