Results of the CAMISIM paper

This repository contains 5 folders:

• coverage_sweep
• figures
• itol
• itol_evaluation
• similarity_ecoli

All the scripts used for creating tables and plots are provided within the repository, alongside the data used for creating them. Internal note: the full data, i.e. all the assemblies and raw data can be found on the BIFO servers under /net/metagenomics/projects/afritz_assemblies

coverage_sweep

Contains the quast output of the coverage sweep data, sorted by error profile (0,2,5% and ART), once with SPAdes and MEGAHIT 1.0.3 and in the subfolder megahit_111 with MEGAHIT 1.1.2

figures

Contains figures for the coverage_sweep and similarity experiment and in the case of similarity the plot to create the panelfig appearing in the CAMISIM paper

itol

Contains the quast results for all the 158 itol genomes, both consensus and strain as subfolder for every genome. Additionally a script summarizing all the three required metrics and the corresponding output files

itol_evaluation

Given the summaries from itol, has the genome fraction values for all genomes sorted by similarity and whether the evaluation was done with the consensus/strain quast, additionally a plot for creating individual plots

similarity_ecoli

Contains the metaquast consensus/strain output for both MEGAHIT 1.0.3 and SPAdes, both for error-free reads and for reads with the ART CAMI error profile