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Raw

SRA status

Descriptions

This directory contains 4 independent pipelines for

  1. Raw nanopore data(FAST5/POD5) availability in SRA database

    Please refer to raw_ONTdata_search.md

  2. BAM availability in SRA database

    Please refer to sra_bam_availability.md

  3. Basecaller version and flowcell version mentioned in SRA database metadata

    We use a multi-thread Python script to analyze the entire metadata set of SRA.

    Specifically, this script first filters the total SRA Runs based on two conditions:

    • the publication date of the SRA Run falls within the range of “2010/01/01” to “2024/01/09”,
    • the sequencing platform is Oxford Nanopore. Multiple regular expressions were then employed to identify keywords related to flowcell or basecaller configuration information within the XML files of the filtered SRA Runs.

  4. Random downsampling SRA run

    Please refer to SRA_random_1000sample.md

Execution environments

Python3 virtual environment

The Python scripts require Python 3.7 or higher. To recreate the same Python running environment use

conda env create -f python3-env.yaml;

Reproduce results

  1. To reproduce our results for pipeline 1 and pipeline 2, please navigate to SRA advanced search in
https://www.ncbi.nlm.nih.gov/sra/advanced

Follow the setting in raw_ONTdata_search.md and sra_bam_availability.md.

  1. To reproduce our results for pipeline 3 and random downsampling part of pipeline 4, run run_all.sh
bash run_all.sh;