Finding metagenomic short read sequences

Question

[eli_bayat]

Hello, I am looking for metagenomic sequencing data in fastq format in order to test my pipeline. I read that I can find these type of data by going to NCBI. I have three questions and appreciate any help.

1. Where or how can I find this data in NCBI?
2. Is there any other sources I can download this type of data?
3. How can I find reference data for antimicrobial resistance mechanism?

Thanks

Answer 1

[Mensur Dlakic]

You can get them at many places. For example, go to https://www.ncbi.nlm.nih.gov/ and type yellowstone metagenome into the search box (or anything that interests you). The result of that search is here. Follow either BioProject or SRA links and you will have hundreds of datasets from which to choose.

Other archives:

• European Nucleotide Archive https://www.ebi.ac.uk/ena/browser/home
• JGI https://img.jgi.doe.gov/ (requires login)

[MSRS]

You can download SRA file by using SRAtoolkit

Answer 2

[Tm]

You can download metagenome data uploaded by people on MG-RAST server for analysis using download option. It also contains analysed result for that data so you can compare your results with MG-RAST's result.