sizemeup is a simple tool to retrieve the genome size for a given species name or tax ID. It utilizes
known genome sizes available from NCBI's Assembly Reports
in combination with user provided genome sizes that may not be available from NCBI.
If you have a species of interest that is not available in the NCBI Assembly Reports, please
consider submitting an issue so that we can get it added to sizemeup. Otherwise, if you have
ideas to improve sizemeup please feel free to!
You can install sizemeup using conda:
conda create -n sizemeup -c conda-forge -c bioconda sizemeup
conda activate sizemeup
sizemeup --helpsizemeup is the main tool that outputs the known genome size for a given species name or tax ID.
sizemeup --help
Usage: sizemeup [OPTIONS]
sizemeup - A simple tool to determine the genome size of an organism
╭─ Required Options ────────────────────────────────────────────────────────────────────╮
│ * --query -q TEXT The species name or taxid to determine the size of [required] │
│ * --sizes -z TEXT The built in sizes file to use [required] │
╰───────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ──────────────────────────────────────────────────────────────────╮
│ --outdir -o PATH Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output files [default: sizemeup] │
│ --silent Only critical errors will be printed │
│ --verbose Increase the verbosity of output │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────╯sizemeup --query "Staphylococcus aureus" --silent
Query Result
┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━┩
│ Staphylococcus aureus │ 1280 │ bacteria │ 2800000 │ ncbi │ manually-set │
└───────────────────────┴───────┴──────────┴─────────┴────────┴──────────────┘
Writing the genome size to .//sizemeup-sizemeup.txt
sizemeup --query 1280 --silent
Query Result
┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━┩
│ Staphylococcus aureus │ 1280 │ bacteria │ 2800000 │ ncbi │ manually-set │
└───────────────────────┴───────┴──────────┴─────────┴────────┴──────────────┘
Writing the genome size to .//sizemeup-sizemeup.txtIf the --query value is found a table is printed to STDOUT as well as to a file named
{PREFIX}-sizemeup.txt where {PREFIX} is the value of the --prefix option (default sizemeup).
Here is an example of the output file:
name tax_id category size source method
Staphylococcus aureus 1280 bacteria 2800000 ncbi manually-setHowever is a species is not found, the you get the following output:
sizemeup --query "escherichia colis" --silent
2024-09-29 20:24:17 ERROR 2024-09-29 20:24:17:root:ERROR - Could not find 'escherichia colis' in the sizes file, sizemeup.py:138
please consider creating an issue at https://github.com/rpetit3/sizemeup/issues to report
this
Query Result
┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┓
┃ Name ┃ TaxID ┃ Category ┃ Size ┃ Source ┃ Method ┃
┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━┩
│ UNKNOWN_SPECIES │ UNKNOWN_TAXID │ UNKNOWN_CATEGORY │ 0 │ UNKNOWN_SOURCE │ UNKNOWN_METHOD │
└─────────────────┴───────────────┴──────────────────┴──────┴────────────────┴────────────────┘
Writing the genome size to .//sizemeup-sizemeup.txtsizemup-build is a helper tool used to build the genome size database for sizemeup. Do do
this it:
- Downloads the latest NCBI Assembly Reports
- Determines species names based on tax id using NCBI Datasets API
- Merges any user provided genome sizes not available from NCBI
Note: This tool isn't necessary for most users, just a simple way to update the database
on your own or at new releases of sizemeup.
In the end, it produces a TSV file with the following columns:
name- the species nametax_id- the NCBI tax idcategory- the category of the species (e.g.bacteria,virus)size- the genome size in base pairssource- the source of the genome size (e.g.ncbi,user)method- the method used to determine the genome size (e.g.automatic,manual)
If you make use of sizemeup in your analysis, please cite the following:
- sizemeup
Petit III RA, Fearing T, Rowley, C sizemeup: A simple tool to determine the genome size of an organism (GitHub)
Talking with Taylor, we have a workflow in Bactopia called
teton for human read scrubbing and taxonomic classification. After running teton, the idea
was to run Bactopia to analyze the samples. However, Bactopia requires a genome size for each
sample in order to calculate coverage and a few other metrics. Sure, we could manually look up
the genome size for each sample, that would be tedious and time consuming. We decided to develop
sizemeup to handle the looking up genome sizes for us. In addition this paves the way for
users of Bactopia to use teton + sizemeup to easily mix species within their runs. In other
words, sizemeup was built to support the Bactopia workflow (but you can use it for whatever!).
As for the name, I wanted something fun and catchy. It's a simple tool to retrieve the genome size of a given species name, so, I thought "sizemeup" would work!
Support for this project came (in part) from the Wyoming Public Health Division.
