Documentation
Compute sequence coverage statistics of motifs from MEME standard XML output
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.
Produce BED12 from BED6 splice junction files.
Find novel splice junctions in RNA-seq data.
Trims sequence and quality string of fastq files on the fly
Modules
A Perl extension for Next-Generation Sequencing data analysis
Object-oriented interface for storing and converting biological sequence annotation formats
Moose wrapper for Bio::DB::Fasta
Provides
in lib/Bio/ViennaNGS/Feature.pm
in lib/Bio/ViennaNGS/FeatureChain.pm
in lib/Bio/ViennaNGS/MinimalFeature.pm