Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data

Area of Science:

• Genomics
• Bioinformatics

Background:

• Short-read sequencing data is commonly stored as aligned reads.
• Aligned data can become outdated with new reference genomes and alignment methods.

Purpose of the Study:

• To introduce Bazam, a tool for extracting original paired FASTQ data from alignment files (BAM/CRAM).
• To enable efficient realignment and reduce computational time for genomic analyses.

Main Methods:

• Bazam extracts paired FASTQ reads from BAM or CRAM files.
• The extracted data is formatted for direct and efficient realignment.

Main Results:

• Bazam reduces realignment time by up to 90% compared to standard methods.
• The tool supports selective extraction of read pairs from specific genomic regions.

Conclusions:

• Bazam provides an efficient solution for updating and re-analyzing outdated alignment data.
• The tool enhances various genomic applications, including targeted analyses and structural variant calling.