Alignment and variant detection: Practical
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This module is dedicated to practicing alignment techniques. Here, you’ll apply what you’ve learned about aligning sequences to reference genomes and work hands-on with alignment tools and data formats like SAM/BAM.
You can use the following files, which are similar to the examples presented in the video.
For the alignment practice you can use the following fastq file and as a reference the fasta file
#Example fastq raw reads
fastq/example.fastq
#Example reference fasta files
fasta/Sars_cov_2.fa
You can also independently review the example VCF files stored in the following folder. Additionally, there is that explains the VCF data format in detail.
vcf/