Fastp
Function
Fastp is a fast and versatile command-line tool for preprocessing high-throughput sequencing data. It is designed to perform quality control, filtering, trimming, and adapter removal in a single step. Fastp supports both single-end and paired-end reads and provides an interactive HTML report for quality assessment.
Input Format
- Technology: Select the sequencing platform (for example, Illumina) so the appropriate adapter and processing defaults are applied.
- Read Type: Select whether the input is single-end or paired-end.
- FASTQ Files: Raw sequence reads in FASTQ format. Both single-end and paired-end reads are supported.
- Adapters (optional): Custom adapter sequences can be provided, or
Fastp can automatically detect and trim them.
Output Format
- FASTQ Files: Cleaned and trimmed sequence reads in FASTQ format.
- JSON Report: A JSON file with detailed statistics about the processing.
- HTML Report: An interactive HTML report summarizing the quality control metrics.
Applications
- Quality Control: Assess the quality of raw sequence reads, including base quality, GC content, and duplication levels.
- Adapter Trimming: Automatically detect and remove adapter sequences from reads.
- Read Filtering and Trimming: Filter out low-quality reads and trim poor-quality bases, improving the overall quality of downstream analyses.
- PolyG Tail Trimming: Remove polyG tails often seen in reads from Illumina platforms.
Example Usage
fastp -i input_R1.fastq -I input_R2.fastq -o output_R1.fastq -O output_R2.fastq -h report.html -j report.json
Suggested Reading
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