BEETL

BEETL-fastq compresses and indexes FASTQ sequencing data to enable efficient storage and rapid k-mer searches within compressed DNA reads.

Key Features:

• Compact Compression: Transforms FASTQ datasets into significantly smaller indexed files with higher compression than gzip and without requiring decompression before use.
• Rapid k-mer Query Search: Performs fast searches for k-mer queries within compressed reads, with query times ranging from milliseconds to minutes depending on complexity and number of queries.
• Direct Output Integration: Returns full FASTQ records for matching reads or read pairs that can be piped into downstream tools for analyses such as variant calling or visualization.
• Scalability and Performance: Scales to datasets containing billions of entries and has been shown to compress 6.6 terabytes of human reads into 1.7 terabytes of indexed files while supporting rapid searches for millions of k-mers.

Scientific Applications:

• Genotyping Structural Variant Breakpoints: Enables identification and genotyping of structural variant breakpoints by locating supporting reads within large sequencing datasets.
• In Silico Pull-down Experiments: Supports selective extraction of reads covering regions of interest for targeted analyses such as variant calling or visualization.

Methodology:

Builds and manipulates indexed, compressed representations of DNA sequences using the Burrows-Wheeler Transform (BWT) to enable efficient storage and rapid search within FASTQ reads.