Rfastp

Rfastp wraps the C++ fastp preprocessor to perform quality control and preprocessing of FASTQ files, including adapter trimming, low-quality base removal, polyX trimming, paired-end read merging, and UMI handling, with support for multiple input files and concatenation.

Key Features:

• Quality Trimming: Removes low-quality bases from FASTQ reads.
• PolyX Trimming: Trims polyX tails from sequences.
• Adapter Detection and Trimming: Auto-detects and trims adapter sequences.
• Paired-End Merging: Merges paired-end reads.
• UMI Handling: Parses UMI sequences and IDs.
• File Concatenation: Concatenates multiple files into one file.
• Multiple File Input: Accepts multiple files as input.

Scientific Applications:

• NGS Preprocessing: Prepares FASTQ data from high-throughput sequencing for downstream analysis.
• UMI-Based Quantification: Enables accurate molecular counting by parsing UMI sequences.

Methodology:

Rfastp is an R wrapper of fastp, which is developed in C++.