additional mock communities to include

caporaso-lab / mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

http://mockrobiota.caporasolab.us

BSD 3-Clause "New" or "Revised" License

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additional mock communities to include #26

Closed gregcaporaso closed 7 years ago

gregcaporaso commented 8 years ago

From Robert Edgar (via feedback on the PeerJ pre-print):

[x] Kozich et al. "dual indexing" V4 HMP mock (doi: 10.1128/AEM.01043-13, FASTQ files: http://www.mothur.org/MiSeqDevelopmentData.html). This is yet another HMP V4 run, but is useful because it has a quite different error profile (presumably due to the different library preparation method).
[x] The "Extreme" community used for DADA2 validation (doi:10.1038/nmeth.3869, SRA run id SRR2990088). This is useful because it has several species which are >97% similar so cannot be resolved by traditional OTU methods.

nbokulich commented 7 years ago

These datasets do not have barcode files. Should we change the travisCI requirements to eliminate the barcode file requirement?

gregcaporaso commented 7 years ago

Should we change the travisCI requirements to eliminate the barcode file requirement?

Yes, I think so. Can we adapt the requirement in some way so there is either a barcodes file or some other scenario (I'm not able to download the files at the moment due to slow wifi connection, so I don't yet have a suggestion for what that requirement could be).

nbokulich commented 7 years ago

Thanks! perhaps we can require a valid barcodes fp if barcodes are listed in the mapping file, or if > 1 sample is listed in the mapping file.

gregcaporaso commented 7 years ago

That should work. Want to make that change? I can review tomorrow when I add the others to Dropbox.

nbokulich commented 7 years ago

Both of these communities (and others) were added with PR #52 . Resolving.