Bio::ViennaNGS 0.12 ============== Bio::ViennaNGS is a distribution of Perl modules and utilities for building efficient Next-Generation Sequencing (NGS) analysis pipelines. It covers various aspects of NGS data analysis, including (but not limited to) conversion of sequence annotation, evaluation of mapped data, expression quantification and visualization. Bio::ViennaNGS is shipped with a complementary set of modules/classes: - Bio::ViennaNGS::AnnoC A Moose interface for storage and conversion of sequence annotation data. - Bio::ViennaNGS::Bam Routines for high-level manipulation of BAM files. - Bio::ViennaNGS::BamStat A Moose-based class for collecting mapping statistics. - Bio::ViennaNGS::BamStatSummary A Moose interface for processing Bio::ViennaNGS::BamStat objects on a set of BAM files. - Bio::ViennaNGS::Bed A Moose interface for manipulation of genomic interval data in BED format. - Bio::ViennaNGS::Expression A Moose interface for computation of normalized gene / transcript expression based on read counts. - Bio::ViennaNGS::ExtFeature A Moose wrapper for extended BED6 elements. - Bio::ViennaNGS::Fasta Routines for accessing genomic sequences implemented through a Moose interface to Bio::DB::Fasta. - Bio::ViennaNGS::Feature A Moose-based BED6 wrapper. - Bio::ViennaNGS::FeatureChain Yet another Moose class for chaining gene annotation features. - Bio::ViennaNGS::FeatureLine An abstract Moose class for combining several Bio::ViennaNGS::FeatureChain objects. - Bio::ViennaNGS::MinimalFeature A Moose interface for handling elementary gene annotation. - Bio::ViennaNGS::SpliceJunc A collection of routines for alternative splicing analysis. - Bio::ViennaNGS::Tutorial A comprehensive tutorial of the Bio::ViennaNGS core routines with real-world NGS data. - Bio::ViennaNGS::UCSC Routines for visualization of genomics data with the UCSC genome browser. - Bio::ViennaNGS::Util A collection of wrapper routines for commonly used third-party NGS utilities, code for normalization of gene expression values based on read count data and a set of utility functions. UTILITIES In addition, Bio::ViennaNGS comes with a collection of utility programs for accomplishing routine tasks often required in NGS data processing. These utilities serve as reference implementation of the routines implemented in the (sub)modules: assembly_hub_constructor.pl: The UCSC genome browser offers the possibility to visualize any organism (including organisms that are not included in the standard UCSC browser bundle) through hso called 'Assembly Hubs'. This script constructs Assembly Hubs from genomic sequence and annotation data. bam_quality_stat.pl: Compute sophisticated quality/mapping statistics for a set of BAM alignment files and produce publication-ready graphics. bam_split.pl: Split (paired-end and single-end) BAM alignment files by strand and compute statistics. Optionally create BED output, as well as normalized bedGraph and bigWig files for coverage visualization in genome browsers (see dependencies on third-patry tools below). bam_to_bigWig.pl: Produce bigWig coverage profiles from (aligned) BAM files, explicitly considering strandedness. The most natural use case of this tool is to create strand-aware coverage profiles in bigWig format for genome browser visualization. bam_uniq.pl: Extract unique and multi mapping reads from BAM alignment files and create a separate BAM file for both uniqe (.uniq.) and multi (.mult.) mappers. bed2bedGraph.pl: Convert BED files to (strand specific) bedGraph files, allowing additional annotation and automatic generation of bedGraph files which can easily be converted to big-type files for easy UCSC visualization. extend_bed.pl: Extend genomic features in BED files by a certain number of nucleotides, either on both sides or specifically at the 5' or 3' end, respectively. gff2bed.pl: Convert RefSeq GFF3 annotation files to BED12 format. Individual BED12 files are created for each feature type (CDS/tRNA/rRNA/etc.). Tested with RefSeq bacterial GFF3 annotation. kmer_analysis.pl: Count k-mers of predefined length in FastQ and Fasta files MEME_xml_motif_extractor.pl: Compute simple statistics from MEME XML output and return a list of found motifs with the number of sequences containing those motifs as well as nice ggplot graphs. newUCSCdb.pl: Create a new genome database to a locally installed instance of the UCSC genome browser in order to add a novel organism for visualization. normalize_multicov.pl: Compute normalized expression data in TPM from (raw) read counts in bedtools multicov format. TPM reference: Wagner et al, Theory Biosci. 131(4), pp 281-85 (2012) sj_visualizer.pl: Convert splice junctions from mapped RNA-seq data in segemehl BED6 splice junction format to BED12 for easy visualization in genome browsers. splice_site_summary.pl: Identify and characterize splice junctions from RNA-seq data by intersecting them with annotated splice junctions. track_hub_constructor.pl: Analogous to assembly_hub_constructor.pl, construct a Track Hub for an organism listed in the UCSC Genome Browser. trim_fastq.pl: Trim sequence and quality string fields in a Fastq file by user defined length. TUTORIAL See Bio::ViennaNGS::Tutorial INSTALLATION To install this module type the following: perl Makefile.PL make make test make install DEPENDENCIES Bio::ViennaNGS and its submodules require a set of third-party libraries and packages that are not part of the Perl core distribution: Bio::Perl >= 1.00690001 Bio::DB::Sam >= 1.37 Bio::DB::Fasta Bio::Tools::GFF File::Share File::Path Template Moose Moose::Util::TypeConstraints Path::Class namespace::autoclean Tie::Hash::Indexed MooseX::Clone MooseX::InstanceTracking The modules listed below are only reuqired by some of the utilities. You will only need to install them if you intend to use the reference utilities: PerlIO::gzip Math::Round XML::Simple Statistics::R Computation of BigWig files from BAM is accomplished via two calls to third-party tools: 'genomeCoverageBed' from the BEDtools suite (http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html) is used to create a BedGraph coverage file at first place. In a second step, the BedGraph is converted to BigWig by 'bedGraphToBigWig', a UCSC Genome Browser utility (http://hgdownload.cse.ucsc.edu/admin/exe/). Please ensure that all third-party utilities are available on your system and accessible to the Perl interpreter. SOURCE AVAILABILITY This source is available on Github: https://github.com/mtw/Bio-ViennaNGS PAPERS If the Bio::ViennaNGS suite is useful for your work or if you use any component of ViennaNGS in a custom pipeline, please cite the following publication: "ViennaNGS - A toolbox for building efficient next-generation sequencing analysis pipelines" Michael T. Wolfinger, Joerg Fallmann, Florian Eggenhofer and Fabian Amman bioRxiv doi: http://dx.doi.org/10.1101/013011 NOTES The Bio::ViennaNGS suite is actively developed and tested on different flavours of Linux and Mac OS X. We have taken care of writing platform-independent code that should run out of the box on most UNIX-based systems, however we do not have access to machines running Microsoft Windows. As such, we have not tested and will not test Windows compatibility. BUGS Please report bugs through the Github issue tracker at https://github.com/mtw/Bio-ViennaNGS/issues AUTHORS Michael T. Wolfinger Joerg Fallmann Florian Eggenhofer Fabian Amman COPYRIGHT AND LICENCE Copyright (C) 2014-2015 Michael T. Wolfinger This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.