SeqPrep

SeqPrep removes adapter sequences and merges overlapping Illumina paired-end reads to produce high-quality input for downstream analyses such as de novo assembly and differential expression studies.

Key Features:

• Adapter Stripping: Removes adapter sequences from raw Illumina reads to prevent interference with downstream analyses.
• Merging Overlapping Reads: Merges overlapping paired-end reads into single contiguous sequences to improve read length and quality.
• Handling Contamination in Mate-Pair Libraries: Detects and merges contaminated mate-pair read pairs when appropriate to address common mate-pair library contamination.

Scientific Applications:

• Transcriptome preprocessing (wheat nitrogen study): Used to filter raw Illumina RNA-seq reads in a wheat study comparing transcriptomes under different nitrogen conditions prior to Trinity assembly and gene prediction.
• De novo transcriptome assembly: Supplies adapter-trimmed and merged reads for de novo assembly using Trinity.
• Quality trimming and differential expression analysis: Acts upstream of quality trimming with Sickle and differential expression analysis with edgeR.
• Functional annotation and pathway analysis: Provides preprocessed reads that support transcript categorization using GO and KEGG.
• Protein-protein interaction network construction: Processed differentially expressed genes have been used to construct protein-protein interaction networks in Cytoscape.

Methodology:

Performs adapter stripping and merging of overlapping paired-end reads, and merges contaminated mate-pair read pairs when appropriate.