Table 1. Overview of the complementary utilities shipped with ViennaNGS.
While some of these scripts are re-implementations of functionality available elsewhere, they have been developed primarily as reference implementation of the library routines to help prospective ViennaNGS users getting started quickly with the development of custom pipelines.
| Utility | Description |
|---|---|
| assembly_hub_constructor.pl | Construct Assembly Hubs for UCSC genome browser visualization |
| bam_quality_stat.pl | Compute mapping/quality statistics along with publication-ready
figures |
| bam_split.pl | Split BAM files by strand |
| bam_to_bigwig.pl | Produce BigWig coverage profiles from BAM files for visualization |
| bam_uniq.pl | Filter uniquely and multi mapped reads from BAM files |
| bed2bedGraph.pl | Convert BED to (strand specific) bedGraph format |
| extend_bed.pl | Extend genomic intervals in BED format at the 5′, 3′, or both ends |
| gff2bed.pl | Convert bacterial RefSeq GFF3 annotation to BED12 format |
| kmer_analysis.pl | Count k-mers of predefined length in FastQ and Fasta files |
| MEME_xml_motif_extractor.pl | Compute basic statistics from MEME XML output |
| newUCSCdb.pl | Create a new genome database in a local UCSC genome browser
instance |
| normalize_multicov.pl | Compute normalized expression data in TPM from read counts |
| sj_visualizer.pl | Convert splice junctions in segemehl BED6 splice junction format to
BED12 |
| splice_site_summary.pl | Identify and characterize splice junctions from RNA-seq data |
| track_hub_constructor.pl | Construct Track Hubs for UCSC genome browser visualization |
| trim_fastq.pl | Trim sequence and quality fields in FastQ format |