# 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](https://www.coursera.org/learn/genomic-tools/lecture/KobfR/alignment-sequence-variation-1-overview)​
2. ​[Alignment and Sequence Variation 2: Alignment and Variant Detection Tools](https://www.coursera.org/learn/genomic-tools/lecture/6DT1v/alignment-sequence-variation-2-alignment-variant-detection-tools)​
3. ​[Alignment and Sequence Variation 3: VCF](https://www.coursera.org/learn/genomic-tools/lecture/pscrb/alignment-sequence-variation-3-vcf)​
4. ​[Alignment and Sequence Variation 4: Bowtie](https://www.coursera.org/learn/genomic-tools/lecture/aZDuX/alignment-sequence-variation-4-bowtie)​
5. ​[Alignment and Sequence Variation 5: BWA](https://www.coursera.org/learn/genomic-tools/lecture/naE7a/alignment-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](https://www.ebi.ac.uk/training/online/courses/human-genetic-variation-introduction/variant-identification-and-analysis/understanding-vcf-format/) that explains the VCF data format in detail.

> vcf/


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