> For the complete documentation index, see [llms.txt](https://edu.abi.am/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://edu.abi.am/ngs-data-analysis-and-functional-genomics/file-formats-alignment-and-genomic-features/sequences-and-genomic-features-part-2-samtools.md).

# Sequences and Genomic Features Part 2: SAMtools

In the previous module, we learned how to perform an alignment to a reference genome and explored the resulting SAM/BAM files generated after alignment. We also covered the main properties of these file formats.

Now, let’s dive into SAMtools, a powerful suite of tools that allows us to efficiently manipulate and analyze these data files.

* [Sequences and Genomic Features 7: SAMtools I](https://www.coursera.org/learn/genomic-tools/lecture/6YQMM/sequences-and-genomic-features-7-samtools-i)
* [Sequences and Genomic Features 8: SAMtools II](https://www.coursera.org/learn/genomic-tools/lecture/GUgmY/sequences-and-genomic-features-8-samtools-ii)

## Materials

You can use the following files, which are similar to the examples presented in the video. 

The files are stored in the following directory on the server:

> sam\_bam/