BIGpre

BIGpre evaluates and preprocesses next-generation sequencing (NGS) data to assess read-level quality and prepare datasets for downstream analyses such as genome assembly, variant calling, and transcriptome profiling.

Key Features:

• Platform Compatibility: Supports Illumina and 454 sequencing platforms.
• Read-level Quality Metrics: Evaluates correlation between forward and reverse reads, analyzes read GC-content distribution, and assesses base N quality.
• Duplicate Read Management: Detects and removes duplicate reads while accounting for sequencing errors.
• Quality Trimming: Trims low-quality reads from raw data.
• Efficient Processing: Processes hundreds of millions of reads within minutes to provide rapid diagnostic information.
• Graphical and Tabular Summaries: Generates tabular and graphical summaries using the R statistics package.
• Implementation: Written primarily in Perl.

Scientific Applications:

• NGS Quality Control: Provides immediate and comprehensive assessment of read-level quality metrics for NGS datasets.
• Genome Assembly: Improves input data quality for genome assembly by removing duplicates and trimming low-quality reads.
• Variant Calling: Supports variant calling by assessing base quality and removing duplicate reads that could bias calls.
• Transcriptome Profiling: Enhances transcriptome analyses by evaluating read quality metrics and trimming low-quality reads.

Methodology:

Computational steps include evaluating forward/reverse read correlation, computing read GC-content distributions and base N quality, detecting and removing duplicate reads with error-aware filtering, performing quality trimming, and producing tabular and graphical summaries via R; the software is implemented primarily in Perl and processes hundreds of millions of reads within minutes.