PyroCleaner

PyroCleaner cleans Roche 454 pyrosequencing reads to remove duplicate, low-complexity, length outlier, and poor-quality sequences and to validate paired-end .sff reads for improved downstream assembly and alignment.

Key Features:

• Read Duplication Filtering: Identifies and removes duplicate reads generated by 454 pyrosequencing bias.
• Length-Based Filtering: Filters sequences by user-specified length criteria to retain reads meeting size requirements.
• Complexity Assessment: Evaluates sequence complexity and filters out low-complexity reads.
• Quality Control: Assesses base-pair quality and filters reads containing a high number of undetermined bases.
• Paired-End Read Cleaning (.sff): Cleans paired-end .sff sequence files, generates validated paired-end sequences, and separates single reads for use as shotgun reads.

Scientific Applications:

• Assembly and Alignment Preparation: Prepares Roche 454 pyrosequencing data for downstream assembly and alignment by removing duplicates, low-quality, and low-complexity reads.
• Paired-End and Shotgun Read Processing: Produces validated paired-end .sff reads and extracts single reads for shotgun analyses.

Methodology:

Computational steps explicitly include duplicate read identification and removal, length-based filtering, sequence complexity evaluation and filtering, base-pair quality assessment to remove reads with many undetermined bases, and cleaning of paired-end .sff files to validate paired reads and separate single reads.