Benchmarking and Simulation Scripts for Plassembler

This directory contains the pipeline used to benchmark Plassembler.

I used Snaketool to make this, and would highly recommend it!

It should work 'out of the box' for the simulated reads. For the real read sets, you will need to change the csv input files in this directory with the correct FASTQ paths of the required files on your system. These FASTQ reads can be found in the Zenodo repository here, or by following the instructions outlined here.

Download plassembler_simulation_benchmarking and install it in a conda env

# creates conda env
conda create -n plassembler_benchmarking pip
conda activate plassembler_benchmarking

# download the repository
git clone "https://github.com/gbouras13/plassembler_simulation_benchmarking"
cd plassembler_simulation_benchmarking

pip install -e .
plassembler_simulation_benchmarking --help

Wick et al., Houtak et al. and Mathers et al. simulated datasets (8 samples)

All outputs will be in a directory called simulated_benchmarking.

simulated_benchmarking will contain SR and LR directories for short and long simulated reads, and SIMULATED containing the Plassembler Flye and Raven and Unicycler outputs for each thread count.

It will also contain BENCHMARKS containing the time/memory etc benchmarks and QUAST, which will contain the Quast outputs comparing Plassembler and Unicycler to the ground truth plasmid assemblies.

Simulate Reads

# creates simulated read sets
plassembler_simulation_benchmarking simulate --input benchmarking_simulate.csv --output simulated_benchmarking --threads 16

Assemble Simulated Reads

# assembles the simulated read sets
plassembler_simulation_benchmarking assemble-simulated --input benchmarking_simulate.csv --output simulated_benchmarking --threads 16

Assess Simulated Read Outputs with Quast

 plassembler_simulation_benchmarking assess-simulated --input benchmarking_simulate.csv --output simulated_benchmarking --threads 16

Wick et al., real datasets (6 samples)

All outputs will be in a directory called real_benchmarking.

real_benchmarking will contain REAL containing the Plassembler Flye and Raven and Unicycler outputs for each thread count.

It will also contain BENCHMARKS containing the time/memory etc benchmarks and QUAST, which will contain the Quast outputs comparing Plassembler and Unicycler to the ground truth plasmid assemblies.

Assemble Real Reads

#### you will need to get the FASTQ files and modify benchmarking_real.csv ####
plassembler_simulation_benchmarking assemble-real --input benchmarking_real.csv  --output real_benchmarking --threads 16

Assess Real Read Outputs with Quast

 plassembler_simulation_benchmarking assess-real --input benchmarking_real_quast.csv --output real_benchmarking --threads 16

De Maio et al. Simulated Dataset (12 samples)

All outputs will be in a directories called simulated_benchmarking_de_maio,

simulated_benchmarking_de_maio will contain SR and LR directories for short and long simulated reads, and SIMULATED containing the Plassembler Flye and Raven and Unicycler outputs for each thread count.

It will also contain BENCHMARKS containing the time/memory etc benchmarks and QUAST, which will contain the Quast outputs comparing Plassembler and Unicycler to the ground truth plasmid assemblies.

Simulate Reads

plassembler_simulation_benchmarking simulate --input benchmarking_simulate_demaio.csv --output simulated_benchmarking_de_maio --threads 16

Assemble Simulated Reads

plassembler_simulation_benchmarking assemble-simulated --input benchmarking_simulate_demaio.csv --output simulated_benchmarking_de_maio --threads 16

Assess Simulated Read Outputs with Quast

 plassembler_simulation_benchmarking assess-simulated --input benchmarking_simulate_demaio.csv --output simulated_benchmarking_de_maio --threads 16