README.md

MGSIM

Metagenome read simulation of multiple synthetic communities

Sections

• REFERENCE
• INSTALLATION
• TUTORIALS
• SIMULATION WORKFLOW
• LICENSE

REFERENCE

DESCRIPTION

Straight-forward simulations of metagenome data from a collection of reference bacterial/archaeal genomes.

Highlights

• Can simulate Illumina, PacBio, and/or Nanopore reads
  • For Illumina, synthetic long reads (read clouds) can also be simulated
• Generate communities differing in:
  • Sequencing depth
  • Richness
  • Beta diversity

The workflow:

• [optional] Download reference genomes
• Format reference genomes
  • e.g., rename contigs
• Simulate communities
• Simulate reads for each community

INSTALLATION

Dependencies

See the conda install line in the CI yaml

Install

via pip

pip install MGSIM

via setup.py

python setpy.py install

Testing

• conda-forge::pytest>=5.3
• conda-forge::pytest-console-scripts>=1.2

In the MGSIM base directory, use the command pytest to run all of the tests.

To run tests on a particular test file:

pytest -s --script-launch-mode=subprocess path/to/the/test/file

Example:

pytest -s --script-launch-mode=subprocess ./tests/test_Reads.py

HOW-TO

See all subcommands:

MGSIM --list

Download genomes

MGSIM genome_download -h

Simulate communities

MGSIM communities -h

Simulate reads for each genome in each community

Simulating Illumina, PacBio, and/or Nanopore reads

MGSIM reads -h

Simulating haplotagging reads (aka read-cloud data)

MGSIM ht_reads -h

LICENSE

See LICENSE