Alignment and variant detection: Practical

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.

1. ​Alignment and Sequence Variation 1: Overview​

2. ​Alignment and Sequence Variation 2: Alignment and Variant Detection Tools​

3. ​Alignment and Sequence Variation 3: VCF​

4. ​Alignment and Sequence Variation 4: Bowtie​

5. ​Alignment and Sequence Variation 5: BWA

Materials

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 a page that explains the VCF data format in detail.

vcf/