How to Align Fastq Files of Sample Genomic DNA Sequence to Reference Genome
Since the aim of this blog is to share the information on various aspects of plants and plant sciences, this time, I am blogging about the bioinformatics tools that help study about the genome of organisms including plants. The application of BWA software or any other software that allows alignment of fastq (.fq) files of the sample genomic DNA sequence to reference genome is an essential step before carrying out further investigations such as the genome analysis. In this post, I am going to present the instruction for the alignment of quality trimmed fastq (.fq) files of a sample genome to the reference genome using BWA (Burrows-Wheeler Aligner) software. This instruction covers installing of BWA software, indexing the reference genome, quality trimming the raw fastq files, and aligning the quality trimmed fastq files to reference genome to get SAM (Sequence Alignment Map) file of a sample genome. Image 1. The vines of Vitis vinifera cv. 'Pinot Noir' with be