Atria

Atria removes adapter sequences and trims low-quality bases from Illumina Next-Generation Sequencing (NGS) reads to improve data integrity for downstream analyses such as variant calling, genome assembly, and transcriptome profiling.

Key Features:

• Ultra-Fast Adapter Trimming: Employs a byte-based matching algorithm that operates in linear time (O(n)) with constant space complexity (O(1)) for rapid adapter identification and removal.
• Multi-Threading Capabilities: Uses multi-threading for sequence processing and file compression to reduce runtime and increase throughput.
• Support for Single-End Reads: Supports trimming of single-end reads in addition to paired-end data.
• Benchmark Performance: Demonstrates superior trimming accuracy and runtime efficiency compared with other trimming tools on simulated and real datasets.
• Broad Application of Matching Algorithm: Applies the byte-based matching algorithm to short-sequence matching tasks such as primer searches and seed scanning prior to alignment.

Scientific Applications:

• Variant Calling: Reduces adapter- and quality-related artifacts that can produce false-positive single nucleotide polymorphisms (SNPs).
• Genome Assembly: Reduces fragmented assemblies by removing adapter contamination and low-quality sequence tails.
• Transcriptome Profiling: Improves reliability of transcriptome analyses by removing adapter sequences and trimming low-quality bases.

Methodology:

Atria uses a byte-based matching algorithm designed for adapter detection that runs in O(n) time with O(1) space and employs multi-threading for sequence processing and file compression.