FastqPuri

FastqPuri preprocesses RNA-seq and other short-read sequencing data by performing quality control, adapter trimming, contamination removal, and quality filtering on FASTQ files.

Key Features:

• Comprehensive Quality Control and Filtering: Executes adapter trimming, contaminant removal, and read-quality filtering to prepare high-quality reads for transcript or gene quantification.
• Contaminant Detection and Removal: Efficiently removes biological contaminants and adapter sequences using flexible filtering strategies optimized for contaminant sequence size.
• Format Versatility: Processes single-end and paired-end reads from compressed or uncompressed FASTQ files.

Scientific Applications:

• High-Throughput Sequencing Preprocessing: Improves data quality for RNA-seq analysis, genome assembly, and single nucleotide variant (SNV) detection by eliminating low-quality and contaminant reads.

Methodology:

FastqPuri applies integrated quality assessment, adapter trimming, and contaminant filtering algorithms implemented in C and R, using size-aware filtering strategies to optimize speed, memory usage, and preprocessing accuracy for short-read datasets.