Skewer

Skewer performs adapter trimming of next-generation sequencing (NGS) reads, identifying and removing adapter sequences from Illumina paired-end, Nextera Long Mate-Pair (LMP), small RNA, genome DNA, and transcriptome RNA/cDNA sequencing data.

Key Features:

• Bit-masked k-difference matching (dynamic programming): Implements a bit-masked k-difference matching algorithm that enumerates candidate adapter alignments within a specified error threshold with expected time complexity O(kn) and space complexity O(m), where k = maximum allowable differences, n = read length, and m = adapter length.
• Statistical scoring scheme: Applies a statistical scoring scheme during pattern matching to evaluate candidate alignments for precise adapter identification and trimming.
• Paired-end and mate-pair optimization: Exploits paired-end and mate-pair information with specialized scoring schemes to improve trimming accuracy, including handling junction adapters located internally as in Nextera LMP.
• Illumina paired-end specialization: Algorithmic design is tailored specifically for processing Illumina paired-end sequencing data.

Scientific Applications:

• Small RNA sequencing: Trims adapters from short fragments to enable accurate small RNA analysis.
• Genome DNA sequencing: Removes adapters from fragments shorter than the read length in genome DNA sequencing workflows.
• Transcriptome RNA/cDNA sequencing: Handles adapter removal for RNA/cDNA fragments shorter than the read length in transcriptome sequencing.
• Nextera Long Mate-Pair (LMP) protocol: Trims junction adapters positioned in the middle of fragments to restore correct paired reads in Nextera LMP libraries.

Methodology:

Skewer combines a dynamic programming, bit-masked k-difference matching algorithm with a statistical scoring scheme and has been validated on simulated and real datasets from small RNA sequencing, paired-end RNA sequencing, and Nextera LMP sequencing.