Solidifying the VirusGraphs Infrastructure for Deployment
insert Charley's figure
Linear references are the gold standard for genomics applications, including capturing viral genome information and viral sequence recovery. Examples include HIV sequence detection and HIV genome assembly. HIV genome assembly can be loosely classified into whole (reference) genome assebly and HIV genotyping (partial assembly).
For nucleobase graphs: NovoGene VG.
For approximate k-mer graphs: original SWIGG, implemented SWIGG.
In the original graph created by SWIGG without any filtering parameters, the number of nodes are usually so large that it would result in inefficient visualization and other downstream analysis. Therefore, we implemented the algorithm to make a compact de Bruijn graph. Contraction of nodes starts by a depth-first-search from the source node of the graph. Nodes are included into a supernode continuously as the algorithm walks through the graph. A new supernode is created when the algorithm encounters a node with more than 1 neighbor. The size of the contracted graph is significantly reduced after contraction algorithm is applied (Table ?).
For split-read mapping, HISAT2 was used, and output .bam was pipped into StringTie, both in Galaxy.
Gephi is used to visualize the output from SWIGG. SnapGene Graphviz
Graphs built with different k-mer lengths:
The above figure contains 5 graphs built with different k-mer lengths. (a) k=16, (b) k=20, (c) k=32, (d) k=50, (e) k=90. Longer k-mers cover more repetitive regions. Therefore, longer k-mers result in simpler graphs. Red rectangles highlights the large loop topology in graphs made by small k-mers. The loops are the results of the repeititive k-mers in regions far apart.
Table of number of nodes and edges before and after contraction
| Before Conrtaction | After Contraction | |||
|---|---|---|---|---|
| kmer | # Nodes | # Edges | # Nodes | # Edges |
| 16 | 38772 | 55265 | 3781 | 4788 |
| 20 | 42442 | 55241 | 2867 | 3641 |
| 32 | 49041 | 55169 | 1350 | 1703 |
| 50 | 52794 | 55061 | 442 | 554 |
| 90 | 54449 | 54821 | 68 | 83 |
Current NovoGraph script.. (TBD).
Figure: cDNA+PCR DNAseq ("classic RNAseq"). A. Coverage summary of reads mapped to HXB2 K03455 with HISAT2 with usegalaxy.eu. B. RmDup-processed reads, controling for PCR duplicates after initial alignment. Search strategy = SRA. Searchterms: "HIV-1 and RNAseq and virus". Bioproject: PRJNA320293, specifically SRR3472915. Viewed in IGV.
Source: From https://github.com/NCBI-Codeathons/Virus_Graphs/edit/master/README.md.
Will add predicted isoform models soon..
Alejandro Gener (Lead/Corresponding Author)
[email protected]; [email protected]
Baylor College of Medicine, Houston, TX, USA
MD Anderson Cancer Center, Houston, TX, USA
Universidad Central del Caribe, Bayamón, PR, USA
Nicolas Cooley
[email protected]
Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh PA, USA,15206
Charles Scott Kirby
[email protected]
Johns Hopkins University School of Medicine, Baltimore, MD, USA
Zhao Liu
[email protected]
Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
Rahil Sethi
Yutong Qiu
[email protected]
Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA