kartzz/ngs repository overview

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 Download SRA sequencing data Convert SRA to FASTQ Compress FASTQ files Run FastQC on raw reads Trim reads using FastP Run FastQC on trimmed reads Generate MultiQC report 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:

Starts SSH service 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 Build