Practical NGS Data Analysis for Variant Calling using Linux

Hands-on NGS Data Analysis Learn Variant Calling using Linux pipeline and perform variant calling easily on command line

What you'll learn:
Gain a solid understanding of Next-Generation Sequencing (NGS) technology and its applications in genomics research.
Learn to set up a bioinformatics environment using Anaconda and install essential tools for NGS data analysis such as FastQC, MultiQC, Samtools, BWA, freebayes,
Acquire skills to find, download, and prepare paired-end FASTQ reads and reference genomes for analysis.
Master the use of FastQC and MultiQC for assessing the quality of raw NGS reads and generating comprehensive quality reports.
Learn to align NGS reads to a reference genome using BWA, and process SAM/BAM files with Samtools for downstream analysis.
Develop proficiency in filtering and processing alignment records, including sorting, indexing, and removing low-quality alignments.
Understand the significance of duplicate reads and learn to mark them using Samtools to ensure accurate variant calling.
Gain hands-on experience in calling genetic variants (SNPs, indels) using Freebayes and generate VCF files for further analysis.
Learn to perform basic statistical analysis on variant calls using bcftools and apply advanced filtering techniques to identify high-confidence variants.
Acquire the skills to conduct a complete NGS data analysis workflow from raw data to variant identification and interpretation.


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