SamTools

SAMtools is a tool for processing SAM files, allowing the extraction of various metrics.

Here is the link to the latest article on the recent improvements of SAMtools.

It was developed by Jhon Marshall and Petr Danecek

For RNA-seq data, Samtools is used in part 4, post-mapping processing. It quantifies the BAM/SAM files.

Figure 1 : simplified RNAseq pipeline.