Vijini Mallawaarachchi

Beauty in Genomics

A collection of assembly graphs from my genomics research, revealing unexpected shapes and patterns in bacterial and phage metagenomes. These figures highlight the visual beauty and complexity of genomic data. Thanks to Bandage for making these assembly graph visualisations possible.

A smiley face formed by colourful genomic graph segments, with two circular eyes and a curved purple smile.

Smiley simPhage

This is the assembly graph of a simulated metagenome containing the phages:

  1. Enterobacteria phage P22 (AB426868)
  2. Enterobacteria phage T7 (NC_001604)
  3. Staphylococcus phage SAP13 TA-2022 (ON911718)
  4. Staphylococcus phage SAP2 TA-2022 (ON911715)

This dataset was used to benchmark Phables.
DOI: 10.1093/bioinformatics/btad586

Assembly graph of the simHC+ metagenome containing 100 bacterial species, with colourful interconnected clusters and smaller disconnected components.

simHC+ metaSPAdes

This is the assembly graph of a simulated metagenome with 100 bacterial species. This dataset was simulated based on the original proportions provided in the MaxBin paper.

This dataset was used to benchmark MetaCoAG.
DOI: 10.1007/978-3-031-04749-7_5

Colourful assembly graph of the ESC simulated bacterial metagenome assembled with metaSPAdes, showing looping paths and interconnected clusters.

ESC metaSPAdes

This is the assembly graph of a simulated metagenome containing the following three bacteria and their corresponding proportions. These were the three most abundant species from the run SRR492184 of the Sharon dataset (NCBI accession number SRA052203).

  1. Enterococcus faecalis - 70.8%
  2. Staphylococcus aureus - 18.9%
  3. Cutibacterium avidum - 3.4%

This dataset was used to benchmark GraphBin.
DOI: 10.1093/bioinformatics/btaa180

Assembly graph wallpaper showing rows of colourful loops, curves, and connected components from a co-assembly of metaviromic samples.

IBD virome assembly graph wallpaper

This is the assembly graph of a co-assembly of metaviromic samples from the study by Norman et al, 2015. The data can be found at NCBI BioProject number PRJEB7772. I often use this as the background for my talk slides.

This dataset was used to benchmark Phables.
DOI: 10.1093/bioinformatics/btad586