ViennNGS

ViennNGS provides processing of next-generation sequencing (NGS) data using an integrated collection of Perl modules to perform feature extraction from NGS file formats, compute read mapping statistics, normalize RNA abundance, identify splice junctions from RNA-seq, parse sequence motifs, construct Assembly and Track Hubs for the UCSC genome browser, and wrap NGS command-line tools for genomic and transcriptomic analysis.

Key Features:

• Perl module collection: An integrated set of reusable Perl modules implements the suite's computational functionality.
• Data extraction and conversion: Extracts and converts features from prevalent NGS file formats for downstream analysis.
• Read mapping statistics: Computes and evaluates read mapping statistics to assess alignment quality and accuracy.
• RNA abundance normalization: Performs normalization of RNA abundance data for comparative analyses across samples.
• Splice junction identification: Identifies and characterizes splice junctions from RNA-seq data to support transcriptome analysis and alternative splicing studies.
• Sequence motif parsing: Parses and condenses sequence motif data to aid identification of regulatory elements.
• UCSC genome browser integration: Automates construction of Assembly and Track Hubs for the UCSC genome browser to enable visualization of genomic data.
• Command-line tool wrappers: Provides wrapper routines for commonly used NGS command-line tools to integrate them into custom workflows.

Scientific Applications:

• Transcriptome analysis: Supports RNA-seq–based transcriptome profiling, including splice-junction detection and transcript characterization.
• Gene expression studies: Enables RNA abundance quantification and normalization for comparative gene expression analysis.
• Genetic variation and regulatory mechanism exploration: Facilitates analysis of mapping statistics, motif discovery, and data visualization to study genetic variation and regulatory elements.

Methodology:

Implemented as reusable Perl modules that extract and convert features from NGS file formats, compute read mapping statistics, normalize RNA abundance, identify and characterize splice junctions from RNA-seq, parse and condense sequence motif data, automate Assembly and Track Hub construction for the UCSC genome browser, and provide wrapper routines for NGS command-line tools.