MetaCRAM

MetaCRAM compresses FASTA and FASTQ metagenomic reads using lossless reference-based methods compatible with CRAM to reduce storage and enable taxonomy-aware retrieval and downstream assembly and analysis.

Key Features:

• Taxonomy Identification and Assembly: Integrates algorithms for taxonomy identification and assembly of metagenomic reads to classify sequences and produce assemblies.
• Lossless Compression: Implements a novel reference-based lossless compression compatible with standard CRAM formats, employing integer compression techniques and empirical distribution fitting of read-reference positions.
• Parallel Execution: Supports parallel execution to run components concurrently for faster processing of large datasets.
• Improved Compression Ratios: Achieves 2- to 4-fold improvements over gzip, with compressed file sizes reduced on average to 2–13% of the original.
• Taxonomy Information Maintenance: Maintains taxonomy information within the compressed domain to allow selection and retrieval of relevant files without full decompression.

Scientific Applications:

• Environmental Microbiology: Analyzing complex microbial communities in soil, water, or air from compressed metagenomic reads.
• Human and Animal Health: Studying microbiomes of human organs and tissues to investigate roles in health and disease using compressed datasets.
• Biotechnology: Facilitating research into microbial functions for industrial applications by enabling efficient storage and transfer of metagenomic data.

Methodology:

Integrates taxonomy identification, read alignment, assembly, and reference-based lossless compression compatible with CRAM, using integer compression techniques and empirical distribution fitting of read-reference positions while maintaining taxonomy information in the compressed domain.