2.0.0

• Kraken2 has replaced BLASTN for the human contig elimination step, to improve speed
• A safety measure has been added to the per-sample MetaSPAdes/SPAdes assembly: If a sample does not successfully assembly within 6 hours, the process will terminate & MEGAHIT will be used to assemble the sample, instead
• Taxonomic profiling is now done with CheckM
• The threads allocated for most rules can be modified from the command line with --config thread_{PROGRAM}={NUMBER}. Please see the configuration file at config/config.yaml for the full list of programs whose thread count can be modified in this manner.
• If a cohort contains both SE and PE reads, the per-cohort assembly will be able to use all three together.
• The initial files needed to run the entire pipeline are now generated as part of the workflow.
• Usage notes/disclaimers:
  • At this stage, most users will need to modify the config.yaml file manually in order to change the reference genome, as well as modify the Snakefile or bash scripts manually in order to change the settings/arguments of the various programs.
  • The workflow has not yet been tested on a SLURM HPC environment, only on a server.

1.0.0-beta

First complete, functional version of the SPOT-BGC pipeline: Build 1.0.0-beta

• The SPOT-BGC pipeline is functional, with the human genome as the reference genome.
• While it has been successfully run for the analysis it was designed for, extensive testing of the pipeline has not been carried out.
• At this stage, users will need to manually modify the config.yaml file in order to change the reference genome, as well as manually modify the Snakefile in order to change the settings/arguments of the various programs.
• Note that the containers used to run the programs are not included in this repository, but should be created by the user as described in the README.md.