q2sra 1.0.0

Fetch, process, analyze, and aggregate microbiome sequencing data with SRA Toolkit and QIIME2.

q2sra

Conventional microbiome bioinformatics workflows are riddled with inefficiencies, as users must navigate a variety of fragmented tools, command-line utilities, and file management systems. In the contemporary research setting, with multiple individuals contribtuting to a singular project, issues with uniformity often arise, complicating subsequent data aggregation/analysis. The q2sra package reconciles these obstacles by providing a streamlined, centralized, and standardized framework for microbiome data analysis with QIIME 2.

Installation

$ pip install q2sra

Prerequisites

• Python v3.11.6+
• QIIME 2 v2023.7+
• SRA Toolkit v3.0.0+

Installing QIIME 2 with Conda

$ wget https://data.qiime2.org/distro/core/qiime2-2023.7-py38-linux-conda.yml
$ conda env create \
    -n qiime2-2023.7 \
    --file qiime2-2023.7-py38-linux-conda.yml
$ rm qiime2-2023.7-py38-linux-conda.yml

Installing SRA Toolkit

Instructions can be found here.

Creating a q2sra Project

To create a project, simply initialize a q2sra.Proj object, supplying the intended project name as the sole parameter.

>>> from q2sra import Proj
>>> proj = Proj('my_proj')

q2sra Project Attributes

Attribute	Type	Default	Description
name	String	None	Project name
fields	List of str	[ ]	Metadata fields
nsamples	Integer	30	Maximum number of samples from each study
paired	Boolean	True	Whether to use forward and reverse reads or exclusively forward reads

Adding Metadata Fields

q2sra.Proj.add_field(field: str, required: bool) -> None

Arguments

• field - Name of field
• required - Whether the field is required [default=False]

Example Run

>>> proj.add_field('Phylum')
>>> proj.add_field('Country', required = True)

Saving a Project

>>> proj.save()

Output

<proj name>.pkl - a pickle file storing the project's attributes.

Loading a Pre-configured Project

Any existing q2sra project saved in .pkl format (see previous step) can later be loaded to perform additional actions (adding more studies, merging runs, etc.).

q2sra.proj.load(name: str) -> None

Arguments

• name - Name of project to load

Example Run

>>> proj = Proj.load('my_proj')

Adding Studies

q2sra.Proj.run(study_name: str, accession: str, include: list, exclude: list) -> None

Arguments

• study_name - Name of study
• accession - Study accession number in the NCBI SRA database
• include - List of substrings that must be included when filtering .fastq files [default=[]]
• exclude - List of substrings that must be excluded when filtering .fastq files [default=[]]

Example Run (w/ user input)

>>> proj.run('takagi_2022', 'PRJNA809527')
Phylum: Chordata
[Required] Country: Japan

Aggregating Studies

After compiling a satisfactory number of studies, individual metadata files and QIIME 2 feature tables/representative sequences can be merged for further analysis using the following method:

>>> proj.merge()