Internship Questions Set Stage 2

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Project 3: Run a simple NGS analysis pipeline

In this section, you will implement a simple NGS analysis on a simple dataset

Starting Datasets:

• Forward Strand
• Reverse Strand
• Reference Genome

Proposed Pipeline:

Download dataset (wget) => Quality Control (FastQC) => Trimming (FastP) => Genome Mapping (bwa) => Variant Calling (bcftools/freebayes)

Feel free to add software as you prefer.

Let’s get bigger:

Use your pipeline to analyze more datasets

Reference: https://raw.githubusercontent.com/josoga2/yt-dataset/main/dataset/raw_reads/reference.fasta

ACBarrie

• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/ACBarrie_R1.fastq.gz
• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/ACBarrie_R2.fastq.gz

Alsen

• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Alsen_R1.fastq.gz
• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Alsen_R2.fastq.gz

Baxter

• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Baxter_R1.fastq.gz
• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Baxter_R2.fastq.gz

Chara

• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Chara_R1.fastq.gz
• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Chara_R2.fastq.gz

Drysdale

• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Drysdale_R1.fastq.gz
• https://github.com/josoga2/yt-dataset/raw/main/dataset/raw_reads/Drysdale_R2.fastq.gz

Submission:

• We look forward to receiving your final pipeline script.sh (you can use bash, snakemake, nextflow or any pipeline tool you know how to use).
• Alongside, create a setup.sh file that anyone can use to install all the tools needed for making the pipeline work.
• Make a requirement.txt file that simply lists all the tools you used
• Upload the 3 files to your team’s github repo. Each team member should have a folder and their folder should contain their 3 scripts.
• Copy the link to the team’s repo and paste it on HackBio Submission platform
• Finally, be ready to discuss your pipeline with everyone

Resources

• Introduction to Whole Genome Sequencing and Variant Calling
• Raw Sequence to Variant Calling Pipeline with FreeBayes (Hands-On)
• Galaxy Tutorial for Variant Calling (with Code)
• Using For loops in BASh
• HackBio Video for loops for multiple datasets using FastP

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