SRA-Data-Collector

The SRA-Data-Collector is a pipeline for downloading samples from NCBI with Metadata. This Snakemake pipeline takes NBCI taxon IDs, study accessions, and run accessions as input and finds all associated samples. Next, it collects metadata for the found samples, which is then cleaned. Finally, the samples are downloaded in parallel.

Instructions

You must install Snakemake with Jupyter notebook support in a conda/mamba environment to run the pipeline. Please refer to the Snakemake documentation for installation instructions.

Snakemake pipelines can be run locally on your computer or on High Performance clusters with job schedulers. Please refer to the Snakemake documentation on how to set up a configuration for specific job schedulers.

Run locally without a config

git clone https://github.com/bayraktar1/reconstruct_plasmids_snakemake.git
cd reconstruct_plasmids_snakemake

# Find samples and collect their metadata
snakemake -s workflow/metadata.smk --cores <number of cores> --use-conda --latency-wait 60 --printshellcmds

# Before downloading, please review the metadata.csv output and make adjustments to the clean.tsv if desired.
snakemake -s workflow/downloads.smk --cores <number of cores> --keep-going --use-conda --latency-wait 60 --printshellcmds

Metadata.smk should NOT be run with --keep-going, all rules should always finish without errors.

Downloads.smk should be run with --keep-going as files belonging to certain accessions might no longer be available, which means that the rule for that accession will fail. This could also occur if a sample is invalid, in which case it will fail during fasterq-dump.

Selecting species & accessions

You can specify NCBI taxon IDs in Data/taxons.txt. Single or multiple taxons can be specified separated by a space. If you specify a taxon ID that belongs to a rank higher than a species, all species of that rank will be downloaded!

Sample accessions and study accessions can be specified in Data/accessions.txt. All samples associated with a study will be collected and downloaded.

You can combine them as long as you specify everything in their respective files.

Samples that fall under "strains" in the NCBi database are currently not found when searching through a higher taxon rank.

Recommendations and warnings

• Please be aware that you could download considerable amounts of samples using this pipeline and run out of storage space quickly.
• It is recommended that you first explore the metadata.csv that is output by the metadata.smk before downloading the samples.
• You can make adjustments to the clean.tsv output to adjust the samples that will be downloaded.
• It is recommended that you pass 10–20 cores to downloads.smk to significantly speed up downloading samples.
• If the download of the SRA database dump fails, you could download it manually from here and place it in the Data/ directory.

Roadmap

• Ensure that samples classified as strains are found by SRA-Data-Collector
• Simplify passing taxon IDs and accessions
• Move away from Snakemake and make an independent package
• Move away from the SRAdb package
• Expand processing of Country names beyond INSDC list with fuzzy searching
• Improve processing of sample sources names by creating categories/groups

License

MIT License

Copyright (c) 2024 Doğukan Bayraktar

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.