ewels/ngi-rnaseq
ewels
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NGI-RNAseq is a bioinformatics analysis pipeline used for RNA-seq data analysis.
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Introduction
NGI-RNAseq is a bioinformatics analysis pipeline used for RNA sequencing data.
It pre-processes raw data from FastQ inputs (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), aligns the reads (https://github.com/alexdo***/STAR or https://ccb.jhu.edu/software/hisat2/index.shtml), generates gene counts (http://bioinf.wehi.edu.au/featureCounts/, https://ccb.jhu.edu/software/stringtie/) and performs extensive quality-control on the results (http://rseqc.sourceforge.net/, https://bioconductor.org/packages/release/bioc/html/dupRadar.html, Preseq, https://bioconductor.org/packages/release/bioc/html/edgeR.html, MultiQC). See the output documentation for more details of the results.
The pipeline is built using [***] a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The pipeline was written at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.
Documentation
The NGI-RNAseq pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Local installation
- Amazon Web Services (aws)
- Swedish UPPMAX clusters
- Swedish cs3e Hebbe cluster
- Tü***gen QBiC
- Adding your own system
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
Credits
These scripts were written at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden. The pipeline was developed by Phil Ewels (https://github.com/ewels) and Rickard Hammarén (https://github.com/Hammarn). Docker and AWS integration was led by Denis Moreno (https://github.com/Galithil) and Phil Ewels (https://github.com/ewels).
Many thanks to other who have helped out along the way too, including (but not limited to): https://github.com/pditommaso, https://github.com/orzechoj, https://github.com/apeltzer, https://github.com/colindaven.
Participating Institutes
NGI-RNAseq is now used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.
| National Genomics Infrastructure (NGI), Sweden | [***] | |
| Quantitative Biology Center (QBiC), Germany | [***] |
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镜像拉取方式
您可以使用以下命令拉取该镜像。请将 <标签> 替换为具体的标签版本。如需查看所有可用标签版本，请访问 标签列表页面。
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DockerHub 原生拉取命令
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