genome-summarize-wf

bit genome-summarize workflow

This is a snakemake workflow for generating and combining genome assembly stats, quality estimates, and taxonomy info. Inputs are fasta files of genome assemblies. For all workflows available with bit, see here.

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• Overview
• Usage
  • Retrieving the workflow
  • Modifying the config.yaml
  • Running the workflow
• Version info

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Overview

This workflow will summarize input genome assemblies, estimate quality, and assign taxonomy via the following programs:

• bit for generating assembly summary stats
• checkm2 for estimating quality of bacteria/archaea
• GTDB-tk for assigning taxonomy of bacteria/archaea
• eukcc for estimating quality of eukarya
• CAT with the NCBI nr database for assigning taxonomy of eukarya

It ultimately produce an output table like this:

Assembly        Total contigs  Total length  Ambiguous characters  GC content  Maximum contig length  Minimum contig length  N50        L50  Est. Completeness (%)  Est. Redundancy (%)  Domain    Phylum          Class                Order             Family             Genus           Species
input_genome_A  1              5,276,633     0                     61.17       5,276,633              5,276,633              5,276,633  1    99.99                  0.96                 Bacteria  Proteobacteria  Gammaproteobacteria  Pseudomonadales   Pseudomonadaceae   Pseudomonas_E   Pseudomonas_E fulva
input_MAG_B     4              2,702,105     0                     33.15       2,601,030              30,881                 2,601,030  1    90.22                  2.78                 Bacteria  Firmicutes      Bacilli              Staphylococcales  Staphylococcaceae  Staphylococcus  Staphylococcus saprophyticus

All required databases will be setup by the workflow if they don't exist already whenever they are used for the first time.

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Usage

bit should be installed via conda as described here.

Retrieving the worklfow

bit-get-workflow genome-summarize

Modifying the config.yaml

Before running it, you first need to set some variables in the config.yaml file (there are notes in there).

The workflow cannot currently run on a mix of input bacteria/archaea genomes and eukaryotic genomes, it can only run on bacteria/archaea by themselves, or eukarya by themselves (as set by a parameter in the config.yaml file).

In the config.yaml file, you mostly just need to point to where the input fasta files are, specify what their extensions are, where the reference databases are stored (or where you want them to go if this is the first time running the workflow), and then you can run the snakemake workflow as exemplified below.

Running the workflow

After variables are set in the config.yaml, here's an example of how it could be run (note that it should still be run inside the bit conda environment):

snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 4 -p

• --use-conda – this specifies to use the conda environments included in the workflow
• --conda-prefix – this allows us to point to where the needed conda environments should be stored. Including this means if we use the workflow on a different dataset somewhere else in the future, it will re-use the same conda environments rather than make new ones. The value listed here, ${CONDA_PREFIX}/envs, is the default location for conda environments (the variable ${CONDA_PREFIX} will be expanded to the appropriate location on whichever system it is run on).
• -j – this lets us set how many jobs Snakemake should run concurrently (keep in mind that many of the thread and cpu parameters set in the config.yaml file will be multiplied by this)
• -p – specifies to print out each command being run to the screen

See snakemake -h for more options and details.

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Version info

Note that the workflows are version independently of the bit package. When you pull one with bit-get-workflow, the directory name will have the version, and it is also listed at the top of the Snakefile.

All versions of programs used can be found in their corresponding conda yaml file in the envs/ directory.