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Life Science

MonetDB/SQL comes with a SAM/BAM module, the de-facto standard for managing DNA sequence alignment data. The module contains the following features to assist SAM/BAM data analysis:

  • Features to load a single SAM/BAM file, a user specified selection of SAM/BAM files, or a complete repository of SAM/BAM files into the database.
  • A database cleanup feature to remove individual SAM/BAM files from the database.
  • A  collection of  SQL functions commonly used in SAM/BAM data analysis, such as computing the reverse complement of a DNA string, and filtering alignment records by their flags.
  • A SAM formatter that renders a database result set into the SAM format

The SAM/BAM modules forms a cornerstone for building lifescience applications around DNA sequences. A quick introduction of the features can be seen in the screencast below, which also demonstrates how MonetDB/BAM works together with popular genomic tools, such as IGV, the Integrative Genomics Viewer.

A specification of the SAM/BAM formats can be found here. Some auxiliary tools for manipulating alignments in the SAM/BAM formats can be found here.