kartzz/ngssalmon repository overview

Short Description

Docker image for automated RNA-Seq transcript quantification using FastQC, FastP, MultiQC, and Salmon with a prebuilt human transcriptome index (Ensembl GRCh38 Release 115).

⁠RNA-Seq Salmon Pipeline Docker Image

⁠Overview

This Docker image provides a complete RNA-Seq quantification workflow for human transcriptome analysis. The image includes commonly used bioinformatics tools and automatically performs quality control, read trimming, and transcript quantification using Salmon.

⁠Included Tools

• FastQC
• MultiQC
• FastP
• Salmon
• HISAT2
• Bowtie2
• BWA
• SAMtools
• BCFtools
• SRA Toolkit
• Python 3

⁠Reference Data

The image automatically downloads:

• Ensembl Human Transcriptome
• Species: Homo sapiens
• Genome Build: GRCh38
• Ensembl Release: 115

A Salmon transcriptome index is generated during image build.

⁠Included Example Dataset

The image downloads and processes:

• SRA Accession: SRR38803505

⁠Pipeline Workflow

1. Download SRA sequencing data
2. Convert SRA to FASTQ
3. Compress FASTQ files
4. Run FastQC on raw reads
5. Trim reads using FastP
6. Run FastQC on trimmed reads
7. Generate MultiQC report
8. Quantify transcripts using Salmon

⁠Directory Structure

/ref ├── Homo_sapiens.GRCh38.cdna.all.fa └── salmon_index

/data ├── *.fastq.gz ├── trimmed/ ├── qc/ └── quants/

/pipeline └── pipeline.py

⁠Build Image

docker build -t rna-seq-salmon-pipeline .

⁠Run Container

docker run -it --rm \
    -p 2222:22 \
    rna-seq-salmon-pipeline

⁠SSH Access

Default credentials:

Username: root

Password: root

Example:

ssh root@localhost -p 2222

⁠Output Files

⁠Quality Control

/data/qc/

Contains:

• FastQC reports
• MultiQC summary report

⁠Trimmed Reads

/ data/trimmed/

Contains:

• Trimmed FASTQ files

⁠Salmon Quantification

/ data/quants/

Contains:

• quant.sf
• cmd_info.json
• aux_info/

⁠Default Command

The container automatically:

1. Starts SSH service
2. Executes the RNA-Seq pipeline

service ssh start && python3 /pipeline/pipeline.py

⁠Notes

• Built on Ubuntu 22.04
• Suitable for RNA-Seq transcript abundance estimation
• Uses automatic library type detection in Salmon (-l A)
• Designed for educational, testing, and small-scale transcriptomics workflows