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qiita-spots / qiita

Qiita - A multi-omics databasing effort
http://qiita.microbio.me
BSD 3-Clause "New" or "Revised" License
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add a per-prep download button for sharing data #3389

Open antgonza opened 3 months ago

antgonza commented 3 months ago

For metaG preps:

For metaT:

AmandaBirmingham commented 3 months ago

Apparently we also need a readme ...

antgonza commented 2 months ago

Just leaving this info here, this is the agreed on README.txt

Delivery created on 05.09.24

Host (human) removal: "human pan-genome reference, with the GRCh38 genome + PhiX and T2T-CHM13v2.0 genome" via "fastp_0.20.1 samtools_1.12  minimap2_2.18"

Main woltka reference: WoLr2, more info visit: https://ftp.microbio.me/pub/wol2/

Qiita's prep: https://qiita.ucsd.edu/study/description/15288?prep_id=16546

Sample information: sample_information_from_prep_16546.tsv
Prep information: 15288_prep_16546_20240321-092136.txt

194427_ec.biom  KEGG Enzyme (EC)
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
194429_per-gene.biom    Per gene Predictions
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
194428_none.biom    Per genome Predictions
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
195908_cell_counts.biom Cell counts
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
    Calculate Cell Counts   https://github.com/qiita-spots/qp-woltka    2023.11 {"SynDNA hits": "194424", "Woltka per-genome": "194428", "min_coverage": "1", "min_rsquared": "0.8", "read_length": "150"}
194430_pathway.biom KEGG Pathway
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
194426_ko.biom  KEGG Ontology (KO)
    Adapter and host filtering v2023.12 https://github.com/qiita-spots/qp-fastp-minimap2    2023.12 {"input": "194422", "reference": "None", "threads": 15}
    SynDNA Woltka   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/databases/synDNA_metagenomic/synDNA_metagenomic", "input": "194423", "min_sample_counts": 1}
    Woltka v0.1.4   https://github.com/qiita-spots/qp-woltka    2023.11 {"Database": "/scratch/qp-woltka/WoLr2/WoLr2", "input": "194425"}
antgonza commented 1 month ago

... also add coverage per table.