GigaDB Dataset - DOI 10.5524/100344 (original) (raw)
In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to interpret this sequence data but none can completely recover the complex information encoded in metagenomes. A number of challenges stand in the way. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in practice. Critically, methodological improvements are difficult to gauge due to the lack of a general standard for comparison. Developers also face a substantial burden to individually evaluate existing approaches, which consumes time and computational resources, and may introduce unintended biases.
The Critical Assessment of Metagenome Interpretation (CAMI) is a community-led initiative that tackles these problems by aiming for an independent, comprehensive and bias-free evaluation of methods. In the first CAMI challenge running from March to July 2015, it provided three simulated benchmark metagenome datasets of different organismal complexities and sizes. These were generated from around ~700 newly sequenced genomes and ~600 circular elements (plasmids, viruses, other circular elements) not included in public databases during the challenge. These are now available here, together with gold standards for assembly, genome and taxonomic binning and taxonomic profiling, the underlying genome sequences, NCBI and ARB reference sequences snapshots from before the challenge and the reference NCBI taxonomy used. In addition, 3 test (toy) data sets are provided that were simulated from public genomes before the challenge. For the most realistic evaluation of reference based methods on the challenge data sets, usually taxonomic binners and profilers, the provided reference sequences or other sequence collections from before challenge should be used as references, as by now all underlying genomes have been deposited at NCBI or EBI.
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Sample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
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CAMI_low | synthetic metagenome | synthetic metagenome | Description:a 15 Gb single sample dataset from a low complexity community with log normal abundance distribution (40 genomes and 20 circular elements; not included in the reference sequence collections also provided in this archive) | 1235509 | |
CAMI_medium | synthetic metagenome | synthetic metagenome | Description:a 40 Gb differential log normal abundance dataset with two samples of a medium complexity community (132 genomes and 100 circular elements; not included in the reference sequence collections also provided in this archive) and long and short insert sizes | 1235509 | |
CAMI_high | synthetic metagenome | synthetic metagenome | Description:a 75 Gb time series dataset with five samples from a high complexity community with correlated log normal abundance distributions (596 genomes and 478 circular elements; not included in the reference sequence collections also provided in this archive) | 1235509 | |
CAMI_TOY_low | synthetic metagenome | synthetic metagenome | Description:a toy data set simulated from public genomes. Can be used for testing tools (gold standards provided). THIS IS NOT A CHALLENGE DATA SET. Genomes: 30 (included in the reference sequence collections also provided in this archive), Total Size: 15 Gbp, Read length: 2x100 bp, Insert size mean: 180 bp, Insert size stddev: 10%. | 1235509 | |
CAMI_TOY_medium | synthetic metagenome | synthetic metagenome | Description:a toy data set simulated from public genomes. Can be used for testing tools (gold standards provided). THIS IS NOT A CHALLENGE DATA SET. Two samples, differential abundance 2 Hiseq (small insert size) differential abundance 15 Gbp samples from 225 genomes (included in the reference sequence collections also provided in this archive). From the same two differential abundance community profiles, 2 Hiseq (5kb insert size) 0.75 Gbp samples | 1235509 | |
CAMI_TOY_high | synthetic metagenome | synthetic metagenome | Description:a toy data set simulated from public genomes. Can be used for testing tools (gold standards provided). THIS IS NOT A CHALLENGE DATA SET. 5 Hiseq (small insert size) 15 Gbp samples (time series) from 450 genomes (included in the reference sequence collections also provided in this archive) 15 Giga base pairs (each sample) Insert size mean: 180 bp Insert size stddev: 18 bp Read length: 2x100 bp | 1235509 |
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File Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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readme_100344.txt | Readme | TEXT | 5.72 kB | 2019-02-26 | MD5 checksum: af5136c9a5e26b4a11b10233da72de6a | |||
CAMI_high.tar | This tar-ball includes the CAMI_high challenge data set and associated information, such as the FASTQ file of the reads for the individual samples, the gold standard assembly, binning and profiling and the genomes from which the samples were simulated. | Mixed archive | TAR | 53.34 GB | 2017-08-11 | MD5 checksum: d7a3a64d9d461ddde15615d1cc71aab7 | ||
CAMI_low.tar | This tar-ball includes the CAMI_low challenge data set and associated information, such as the FASTQ file of the reads for the individual samples, the gold standard assembly, binning and profiling and the genomes from which the samples were simulated. | Mixed archive | TAR | 11.25 GB | 2017-08-11 | MD5 checksum: 0c2259e190d308a3f3006910f5086632 | ||
CAMI_medium.tar | This tar-ball includes the CAMI_medium challenge data set and associated information, such as the FASTQ file of the reads for the individual samples, the gold standard assembly, binning and profiling and the genomes from which the samples were simulated. | Mixed archive | TAR | 28.41 GB | 2017-08-11 | MD5 checksum: f15dfeadbe7536ad410ba8f3129ae746 | ||
taxonomy.tar.gz | Taxonomy database as of 2015/06/22 to be used for CAMI challenge datasets | Mixed archive | TAR | 26.47 MB | 2017-08-11 | MD5 checksum: 7752be09d97662b48e10b501901d418d | ||
camiClient_taxdb.tar.gz | Taxonomy database to be used for cami upload client | Mixed archive | TAR | 94.65 MB | 2017-08-11 | MD5 checksum: 238b36b6e8febd068b35715e655f9182 | ||
225_genomes.tar | This tar-ball includes all CAMI_TOY_medium data sets, such as the FASTQ file of the reads, the gold standard assembly, binning and profiling. | Mixed archive | TAR | 33.56 GB | 2017-08-11 | MD5 checksum: 4cc0db87294a8b09b7615ae4b591881a | ||
30_genomes.tar | This tar-ball includes all CAMI_TOY_low data sets, such as the FASTQ file of the reads, the gold standard assembly, binning and profiling. | Mixed archive | TAR | 15.41 GB | 2017-08-11 | MD5 checksum: eb14193df45fe4fa9901202269ad573d | ||
450_genomes.tar | This tar-ball includes all CAMI_TOY_high data sets, such as the FASTQ file of the reads, the gold standard assembly, binning and profiling. | Mixed archive | TAR | 80.53 GB | 2017-08-11 | MD5 checksum: 6815d7c5f74942484a2cc95bb878f1a7 | ||
PROCESSED_NCBI.tar | This tar-ball is a copy of the NCBI Refseq and Taxonomy Database as of 2015/06/22. This database should be used as a basis for reference based binning and profiling tools for the CAMI challenge datasets. | Mixed archive | TAR | 158.03 GB | 2017-08-11 | MD5 checksum: d7f20a92c76458cc885344f52a28b1d4 |
Date | Action |
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August 11, 2017 | Dataset publish |
February 26, 2019 | File program_results.tar.gz updated |
February 26, 2019 | File readme_100344.txt updated |
February 26, 2019 | readme_100344.txt: file attribute updated |
February 26, 2019 | File readme_100344.txt updated |
February 26, 2019 | program_results.tar.gz: additional file attribute added |
February 26, 2019 | File program_results.tar.gz updated |
June 14, 2023 | Relationship added : DOI 102408 |