CAMISIM_reproducibility

To reproduce some results from "CAMISIM: simulating metagenomes and microbial communities".
Authors: Simon Konnov, Ciara Makievskaya, Ruslan Gumerov

commands.txt contains all commands which were used in current research.
visualisation_plots.ipynb contains all commands which were used to visualize our results. Every 3 plots belong to different accemblers (megahit 1.0.3, megahit 1.1.2, metaSPAdes 3.12.0).
data contains pair-ended reads with 2x coverage (for example; during our project we worked also with 4x, 8x, 16x, 32x, 64x, 128x (256x and 512x also for megahit 1.1.2) coverages) and different error rates (0%, 2%, 5%) generated with wgsim.
bandage contains MEGAHIT 1.0.3 assembly graphs (k = 41) of an E. coli K12 genome for 2× and 32x per-base coverage visualized with Bandage (on a different scale)