Documentation

Construct a UCSC genome browser TrackHub
Build UCSC genome browser Assembly Hubs from genomic sequence and annotation
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
Get nucleotde and amino acid sequences from BED intervals
Convert BED6 to BED12.
Extract individual sequences from a multi Fasta file
Find sequence motifs in a (multi) Fasta file
Extract subsequence from a (multi) Fasta file
Convert (non-spliced) GFF3 to BED12
Simple k-mer count analysis of fasta or fastq files
Compute normalized expression data from read counts
Identify peaks/enriched regions in RNA-seq data
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
Trim 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
Object-oriented interface for manipulation of genomic interval data in BED format
An object oriented interface for computing read-count based gene expression as TPM or RPKM
A Moose wrapper for extended BED6-type genomic intervals.
Moose wrapper for Bio::DB::Fasta
A Moose wrapper for BED6-type genomic intervals.
A Moose Role for BED compliance
Generic Moose wrapper class for combined/linked genomic intervals, eg BED12 elements
Versatile I/O interface for Bio::ViennaNGS feature annotation classes
A Moose class for unstranded, elementary genomic intervals.
A Moose wrapper for named genomic intervals.
A Moose wrapper for stranded genomic intervals.
An object oriented interface for characterizing peaks in RNA-seq data
Perl extension for alternative splicing analysis
A collection of basic tutorials demonstrating of the core components and features of the Bio::ViennaNGS suite
Perl extension for easy UCSC Genome Browser integration.
Utility routines for Next-Generation Sequencing data analysis