File:Fig2 Backman BMCBio2016 17.gif

Figure 2. Workflow Steps and Graphical Features. Relevant workflow steps of several NGS applications (a) are illustrated in form of a simplified flowchart (b). Examples of systemPipeR’s functionalities are given under (c) including: (1) eight different plots for summarizing the quality and diversity of short reads provided as FASTQ files; (2) strand-specific read count summaries for all feature types provided by a genome annotation; (3) summary plots of read depth coverage for any number of transcripts with nucleotide resolution upstream/downstream of their start and stop codons, as well as binned coverage for their coding regions; (4) enumeration of up- and down-regulated DEGs for user defined sample comparisons; (5) similarity clustering of sample profiles; (6) 2-5-way Venn diagrams for DEGs, peak and variant sets; (7) gene-wise clustering with a wide range of algorithms; and (8) support for plotting read pileups and variants in the context of genome annotations along with genome browser support.

Backman, T.W.H.; Girke, T. (2016). "systemPipeR: NGS workflow and report generation environment". BMC Bioinformatics 17: 388. doi:10.1186/s12859-016-1241-0. 

2016

Backman, T.W.H.; Girke, T.

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