sam

SAM (Sequence Alignment/Map) is a command line tool used for manipulating and analyzing sequence alignment data. It allows users to process high-throughput sequencing data, such as DNA or RNA sequences, by aligning them to a reference genome. SAM tools are commonly used in genomics research and bioinformatics analysis. One important feature of SAM is its ability to convert between different file formats commonly used in sequencing analysis, such as SAM, BAM, and CRAM. SAM provides a range of functionalities, including sorting and filtering sequence alignments based on various criteria, such as read qualities or mapping scores. It allows for the extraction of sequencing reads aligned to a specific region or set of regions in the reference genome. Additionally, SAM tools offer functions for analyzing coverage and depth of sequencing, as well as generating statistics about the alignment results. This can be useful in variant calling, identifying genomic variations between different samples. SAM tools are implemented in C programming language and are highly optimized for performance. They can efficiently handle large-scale sequencing datasets and are widely used in the field of genomics research.