SAM (file format)

SAM (file format) is a text-based file format used to store biological sequences aligned against a reference sequence. SAM stands for Sequence Alignment/Map format. It is widely used in bioinformatics for storing large volumes of genomic data. The format was developed to work with sequencing data from various sources, such as DNA sequencing and RNA sequencing. SAM files are crucial for researchers analyzing genetic variations and understanding complex genetic structures in organisms.

Overview

The SAM format is a flexible and comprehensive way to represent sequence alignments, allowing for efficient data analysis and manipulation. It consists of a header section and an alignment section. The header section contains information about the version of the format, the reference sequence, and other metadata. The alignment section describes the alignment of each read to the reference sequence, including the position, mapping quality, and the actual sequence data.

Features

• Text-based: SAM files are plain text, making them easy to read and edit with standard text editors.
• Comprehensive: They can store not just the alignment information but also additional attributes for each alignment, such as mapping quality, editing distance, and optional tags for further details.
• Flexible: SAM format supports various sequencing technologies and applications, making it a versatile choice for different types of genomic analyses.

Usage

SAM files are primarily used in bioinformatics for tasks such as:

• Genome assembly: Assembling short sequencing reads into longer sequences that represent the organism's genome.
• Variant calling: Identifying variations in the genomic sequence, such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels).
• Read mapping: Aligning sequencing reads to a reference genome to identify where in the genome the reads came from.

Related Formats

The Binary Alignment/Map (BAM) format is a binary version of the SAM format. BAM files are more compact and faster to process but are not human-readable without conversion. The conversion between SAM and BAM formats is facilitated by tools like SAMtools, a suite of programs for interacting with high-throughput sequencing data.

Tools and Software

Several bioinformatics tools and software packages support the SAM format, including:

• SAMtools: A suite of utilities for manipulating alignments in the SAM format, including sorting, merging, indexing, and converting between SAM and BAM.
• Picard tools: A set of Java-based command-line utilities that manipulate SAM files, including sorting, validation, and duplicate marking.
• IGV (Integrative Genomics Viewer): A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Conclusion

The SAM file format plays a critical role in the field of bioinformatics, enabling the storage, analysis, and sharing of sequence alignment data. Its flexibility and comprehensiveness make it an essential tool for genomic research, facilitating advances in understanding genetic information and its implications for health and disease.

SAM (file format) Resources
Latest articles Most recent articles Ongoing trials	Wikipedia