Btrim

Btrim trims adapters, detects low-quality regions, and assigns barcodes in reads from ultra high-throughput next-generation sequencing (NGS) platforms to preprocess sequencing data for downstream analysis.

Key Features:

• Adapter trimming: Removes adapter sequences from reads and supports multiple sets of adapter pairs simultaneously.
• Quality trimming: Identifies and removes low-quality regions from either or both ends of reads.
• Barcode assignment: Assigns barcodes to their corresponding original samples for demultiplexing.
• Indel-aware matching: Uses a modified version of Myers's bit-vector dynamic programming algorithm to handle insertions and deletions (indels) in adapters and barcodes.
• Performance: Processes approximately 30 million reads with two sets of adapter pairs in about one minute while maintaining a minimal memory footprint.

Scientific Applications:

• Transcriptomics: Preprocesses RNA-seq reads by removing adapters and low-quality bases prior to expression analysis.
• Metagenomics: Cleans and demultiplexes environmental sequencing reads for community composition and assembly workflows.
• Epigenetics: Prepares bisulfite or other epigenomic sequencing reads by trimming adapters and filtering low-quality regions.
• NGS preprocessing: Serves as an initial preprocessing step in NGS analysis pipelines to improve data quality for downstream analyses.

Methodology:

Performs adapter trimming, low-quality region detection and removal from either or both ends, barcode assignment, and multiple-adapter handling using a modified Myers's bit-vector dynamic programming algorithm to accommodate insertions and deletions (indels) in adapters and barcodes.