NxTrim

NxTrim trims 38-bp adapter sequences produced by the circularization-based Nextera Mate Pair (NMP) protocol and reconstructs virtual libraries to recover mate-pair, paired-end, and single-end reads for improved genome assembly.

Key Features:

• Adapter Trimming: Identifies and removes 38-bp adapter sequences from reads generated by the circularization-based NMP protocol while minimizing loss of adjacent genomic sequence.
• Virtual Libraries Construction: Uses sequence information flanking the adapter site on both sides to classify reads into mate pairs, paired-end reads, and single-ended reads, producing virtual libraries.
• Data Preservation: Preserves maximal genomic sequence adjacent to the adapter site to reduce discarded bases from NMP reads and retain data for downstream analysis.

Scientific Applications:

• Genome assembly and scaffolding: Facilitates assembly by providing virtual libraries that help bridge larger repeats and resolve complex genomic regions.
• Bacterial genome sequencing: Enables assemblies of bacterial genomes with quality comparable to those derived from traditional paired-end reads.

Methodology:

Analyzes sequence on both sides of the adapter site to accurately identify and trim adapters while preserving adjacent genomic information, then assigns reads to virtual libraries (mate-pair, paired-end, single-end) based on adapter position.