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Where can I get Human microbiome dataset

There used to be this place where microbiome dataset were stored. However, the link seems to be no longer working. Are the data no longer accessible or can I find the data somewhere else? I understand Qiita is another source but the previous person in my lab used HMP data and I am in need of them to reproduce some experiments. Thank you!

microbiome human data
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updated by Arup Ghosh Arup Ghosh • written by Emily • Emily

2 answers

I assume the sample should be available in SRA. Do you know the accessions of some of the samples?

If the data is available from Qiita then by all means it should be equivalent.

Sad to see HMPDACC site disappear without any trace.

Note: Found main SRA project https://www.ncbi.nlm.nih.gov/bioproject/28331 and parent https://www.ncbi.nlm.nih.gov/bioproject/43021

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written by GenoMax GenoMax

Unfortunately I don't. I was recommended to use HMP becausee Qiita doesn't have the same data as HMP....

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written by Emily • Emily

The processed files can be found in the following AWS S3 links.(hmsmcp V2)

$ aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/community_prof/metaphlan2_2017/hmp1-II_metaphlan2-mtd-qcd.pcl.bz2 . --no-sign-request 
$ aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/metabolic_prof/humann2_2017/hmp1-II_humann2_pathabundance-nrm-mtd-qcd.pcl.bz2 . --no-sign-request
$ aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/metabolic_prof/humann2_2017/hmp1-II_humann2_pathcoverage-mtd-qcd.pcl.bz2 . --no-sign-request

Raw datasets

s3://hmpdcc/hmp1/hhs/microbiome/wms/raw/

Assemblies and v1, v2 processed (Source: https://github.com/IGS/portal_client/issues/33#issuecomment-2673340590)

hmwgsqc v1 - aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/qc/qc_2012/ . --no-sign-request
hmwgsqc v2 - aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/qc/qc_2017/ . --no-sign-request
hmasm - aws s3 cp s3://hmpdcc/hmp1/hhs/microbiome/wms/analysis/assemblies/single_sample/ssasm_2012/ . --no-sign-request

Browse the AWS buckets

https://42basepairs.com/browse/s3/hmpdcc/ihmp
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written by Arup Ghosh Arup Ghosh

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