WGS EQA

A set of tools for external quality assurance for pathogen sequencing

Dependencies

• Python 3
• Numpy
• Biopython

Contents

1. Simulate

1.Simulate

Generates a simulated reference sequence from an existing reference sequence. Allows for mutations, recombination events, and indels to be simulated.

Example usage

bin/simulate_reference.py -r ref/R00000003.fasta -o example_output/R00000003 -m 500 -s 300 -l 1000 -p 0.04 -d 100 -e 1.5 -i 100 -n 1.5

Example usage, simulating mutations only

bin/simulate_reference.py -r ref/R00000003.fasta -o example_output/R00000003 -m 500 -s 0 -d 0  -i 0

Obtain help

bin/simulate_reference.py -h
usage: simulate_reference.py [-h] -r REF_FILE -o OUTPUT [-m MUTATION_N]
                             [-s SUBS_FROM_RECOMB] [-l RECOMB_LENGTH_MEAN]
                             [-p PROP_OF_SITES_DIFF_IN_RECOMB] [-d DELETION_N]
                             [-e DELETION_LENGTH_MEAN] [-i INSERTION_N]
                             [-n INSERTION_LENGTH_MEAN]

Simulate a new reference from an existiing reference with mutation,
recombination, indels

optional arguments:
  -h, --help            show this help message and exit
  -r REF_FILE, --refile REF_FILE
                        path to existing reference file
  -o OUTPUT, --output OUTPUT
                        path stem for new reference file
  -m MUTATION_N, --mutation_n MUTATION_N
                        expected number of mutation events (including same
                        base to same base)
  -s SUBS_FROM_RECOMB, --subs_from_recomb SUBS_FROM_RECOMB
                        expected number of substitutions from recombination
                        events (including same base to same base)
  -l RECOMB_LENGTH_MEAN, --recomb_length_mean RECOMB_LENGTH_MEAN
                        mean recombination fragment length
  -p PROP_OF_SITES_DIFF_IN_RECOMB, --prop_of_sites_diff_in_recomb PROP_OF_SITES_DIFF_IN_RECOMB
                        proportion of sites substituted in recombination
                        fragment (includng same to same)
  -d DELETION_N, --deletion_n DELETION_N
                        mean number of deletion events
  -e DELETION_LENGTH_MEAN, --deletion_length_mean DELETION_LENGTH_MEAN
                        mean length of deletion event (geometrically
                        distributed)
  -i INSERTION_N, --insertion_n INSERTION_N
                        mean number of insertion events
  -n INSERTION_LENGTH_MEAN, --insertion_length_mean INSERTION_LENGTH_MEAN
                        mean length of insertion event (geometrically
                        distributed)

Docker implementation

This will run the simulation for a given set of parameters, and then run wgsim to generate gzipped fq simualted read files.

Requires a local installation of

• Docker - https://www.docker.com/get-started
• Java version 8 or later (required for nextflow)
• Nextflow - https://www.nextflow.io

This can be pulled from docker hub

docker pull davideyre/wgs-eqa

Run the workflow, with appropriate settings, e.g.:

nextflow run simulate.nf --outputPath ../pipeline-test/sim-ref --refFile ref/R00000003.fasta

Following this you can use the script provided to generate a summary of the simulations and simulated reads for input into a WGS pipeline:

bin/collect_simulations.py -p ../pipeline-test/sim-ref/ -o ../pipeline-test/sim-list.csv

These can then be run using BUGflow (http://github.com/davideyre/bug-flow), like this

cd bug-flow
nextflow run bug-flow.nf -profile server \
	--seqlist ../pipeline-test/sim-list.csv \
	--outputPath ../pipeline-test/bug-flow-output \
	--refFile ../wgs-eqa/ref/R00000003.fasta \
	--runSpades 0

David Eyre david.eyre@bdi.ox.ac.ul 25 January 2019