clean_ngs

clean_ngs performs preprocessing of next-generation sequencing (NGS) reads by removing adapter sequences and trimming low-quality bases to improve data quality for downstream genomic analyses.

Key Features:

• Adapter Trimming: Uses a user-defined adapters definition file (ADAPTER.txt) to identify and remove adapter sequences from input reads.
• Quality Filtering: Trims nucleotides from both the 5' and 3' ends of reads based on quality score thresholds to remove low-quality bases.
• Output Management: Produces two output files separating cleansed reads from rejected reads that did not meet the specified criteria.

Scientific Applications:

• Metagenomics: Preprocesses reads to remove adapters and low-quality bases prior to taxonomic profiling and functional analysis.
• Phylogenetics: Improves sequence quality for accurate phylogenetic inference by removing sequencing artifacts and low-quality regions.
• Downstream alignment and assembly: Generates higher-quality input for read alignment and genome or transcriptome assembly workflows.

Methodology:

References an adapters definition file (ADAPTER.txt) to identify and excise adapter sequences, applies quality-score thresholds to trim low-quality nucleotides at both 5' and 3' ends of reads, and segregates outputs into cleansed and rejected read files.