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Documentation

Generates a simple statistic with ggplots about the sequence coverage of motifs from MEME standard xml output
An example pipeline for the ViennaNGS toolbox
Build UCSC genome browser Assembly Hubs from genomic sequence and annotation
Generates quality statistics from specified BAM input files.
Split a BAM file by strands
Make bigWig coverage profiles from BAM files
Deconvolute BAM files into unique and multi mappers
Convert BED or extended BED files to bedGraph format
Extends bed entries strand specific one- or two-sided.
Convert (non-spliced) GFF3 to BED12
Simple k-mer count analysis of fasta or fastq files
Find sequence motifs in annotated features.
Compute normalized expression data from read counts
Produce BED12 from BED6 splice junction files.
Find novel splice junctions in RNA-seq data.
Build UCSC genome browser Track Hubs from genomic sequence and annotation
Trims sequence and quality string of fastq files on the fly

Modules

A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Object-oriented interface for storing and converting biological sequence annotation formats
High-level access to BAM files
Moose interface to BAM mapping statistics
Object-oriented interface for manipulation of genomic interval data in BED format
An object oriented interface for read-count based gene expression
Moose wrapper for Bio::DB::Fasta
Perl extension for alternative splicing analysis
An example pipeline for the ViennaNGS toolbox
Perl extension for easy UCSC Genome Browser integration.
Utility routines for Next-Generation Sequencing data analysis

Provides

in lib/Bio/ViennaNGS/BamStatSummary.pm
in lib/Bio/ViennaNGS/Feature.pm
in lib/Bio/ViennaNGS/FeatureChain.pm
in lib/Bio/ViennaNGS/MinimalFeature.pm