SAMBLASTER

SAMBLASTER marks duplicate reads in read-sorted SAM output from Illumina DNA aligners and extracts discordant read-pairs and split-read mappings to support structural variant calling while minimizing I/O before BAM compression.

Key Features:

• Duplicate marking: Marks duplicates in read-sorted SAM files during a piped post-pass on DNA aligner output prior to BAM compression.
• Discordant and split-read extraction: Concurrently extracts discordant read-pairs and split-read mappings for structural variant callers.
• I/O reduction: Minimizes repetitive reading, writing, sorting, and compressing of SAM/BAM files to reduce computational overhead.
• Alignment post-pass integration: Operates as an alignment post-pass that integrates into existing pipelines with minimal additional runtime overhead.
• Performance: Produces duplicate-marked results nearly identical to PICARD and SAMBAMBA while using less time and memory.
• Implementation: Implemented in C++.

Scientific Applications:

• Structural variant discovery: Supplies discordant pair and split-read evidence required by structural variant calling methods.
• Variant calling workflows: Provides duplicate-marked alignments to improve accuracy of downstream variant calling analyses.
• High-throughput sequencing pipelines: Reduces I/O bottlenecks in Illumina DNA sequencing pipelines to enable scalable processing of large BAM files.

Methodology:

Marks duplicates in read-sorted SAM during a piped post-pass on DNA aligner output prior to BAM compression and concurrently extracts discordant read-pairs and split-read mappings; implemented in C++.