Bazam

Bazam is a computational tool that addresses the challenges associated with the continuous evolution of reference genomes and alignment methods in analyzing short-read sequencing data. Given that sequencing data are frequently exchanged and stored as aligned reads, the need for efficient tools to revert these aligned reads back to their original paired FASTQ format for subsequent realignment becomes critical. This need arises because aligned data may become outdated with the development of new reference genomes and more sophisticated alignment techniques.

Bazam steps into this space by offering an efficient mechanism to extract the original paired FASTQ files from alignment files, specifically those in BAM or CRAM format. This capability is significant for ensuring that sequencing data can be realigned efficiently, leveraging the latest genomic references and alignment algorithms to enhance the accuracy of genomic analyses.

A significant advantage of using Bazam is the dramatic reduction in the time required for realignment processes. The tool facilitates up to a 90% decrease in realignment time compared to conventional methods, representing a substantial improvement in efficiency for genomic researchers and bioinformaticians dealing with large datasets.

Beyond its core functionality, Bazam supports selective extraction of read pairs from specific genomic regions. This feature is invaluable for various applications, including targeted region analyses, quality control measures, structural variant calling, and comparisons between different alignment methods. By enabling focused analysis on particular regions of interest, Bazam enhances the efficiency of genomic analyses and contributes to the depth and precision of such investigations.