AlienTrimmer

AlienTrimmer removes contaminant oligonucleotide sequences (e.g., primers and adapters) from FASTQ-formatted high-throughput sequencing reads to improve the accuracy of downstream analyses.

Key Features:

• Contaminant detection and removal: Identifies and excises contaminant sequences that occur at one or both ends of sequencing reads.
• K-mer decomposition: Decomposes specified alien nucleotide sequences into k-mers (subsequences of length k) to enable contaminant detection.
• Polynomial algorithm: Employs a simple polynomial-time algorithm to determine occurrence of contaminant k-mers at read ends.
• Read format and end handling: Operates on FASTQ-formatted reads and supports detection in single-end and paired-end files.
• Platform compatibility: Validated on Illumina®, 454™, and Ion Torrent™ sequencing data.
• Performance and accuracy: Capable of processing millions of reads within minutes while maintaining high precision in contaminant removal.

Scientific Applications:

• Genome assembly: Improves assembly accuracy by removing primer and adapter contaminants from input reads.
• Variant calling: Reduces false-positive variant calls caused by residual adapter or primer sequences.
• Transcriptome profiling: Enhances quantification accuracy by eliminating contaminating oligonucleotides.
• Metagenomic studies: Decreases spurious taxonomic assignments by removing non-biological sequence contaminants.

Methodology:

Decomposition of specified contaminant sequences into k-mers; use of a polynomial-time algorithm to detect these k-mers at read ends in FASTQ single-end and paired-end files.