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CAMI-challenge / AMBER

AMBER: Assessment of Metagenome BinnERs
https://cami-challenge.github.io/AMBER/
GNU General Public License v3.0
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a data-related problem #45

Closed Huangpq2019 closed 3 years ago

Huangpq2019 commented 3 years ago

Dear, In the article "Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit", the CAMI II mouse gut dataset used is the short reads of 64 samples? If so, where can I download this dataset? I only found pacbio scaffolds related data in https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/CAMISIM_MOUSEGUT, but no short reads.

Looking forward to your reply, thanks!

fernandomeyer commented 3 years ago

Yes, the CAMI II mouse gut short-read data were used and made available. To get the full list of files, use the command:

java -jar camiClient.jar -l https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/CAMISIM_MOUSEGUT

The short reads are in the following files:

19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz
19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz
...
19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_63/reads/anonymous_reads.fq.gz

The gold standard cross-sample assembly is in: 19122017_mousegut_scaffolds/anonymous_gsa_pooled.fasta.gz

The dataset is also available at https://doi.org/10.4126/FRL01-006421672 (though Publisso's download link appears to be temporarily broken).