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.

Supplementary Data S3: Brycon orbignyanus (Characiformes: Bryconidae) draft partial genome assembly (~10X) in fasta format (.fsa). Assembled from Illumina HiSeq 2000 short reads (retrievable from NCBI-SRA SRX3350440), using SOAPdenovo 2 (k-mer=55) with the intention to screen for microsatellite loci. This assembly A1 was the base for the alignments performed with SOAPaligner retrivable from NCBI-SRA SRX3427716).
The final size of the genomic assembly A1 is 1,113,754,917 bp (including unknown base calls and gaps, N) and 1,039,212,289 bp (not counting Ns – Δ=74,542,628). A total of 1,273,306 contigs or scaffolds were obtained, the shortest being 100 bp and the longest 172,138 bp (average=874). Only 55 scaffolds were longer than 100 kbp; 1.97% longer than 10 kbp; 11% longer than 1 kbps and 18.09% of 500 bp or more. The A1 assembly had the CG content of 41.18% and N50=8,463.
These results are part of the article "A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae), an endangered migratory Neotropical fish". Scientific Reports, 8: 8511, 2918

Supplementary Table S2 - A broad genomic panel with potentially amplifiable microsatellite loci for Brycon orbignyanus is publicly made available. Loci marked with an asterisk (*) have been empirically validated as polymorphic (Arias et al., 2016; Conservation Genetics Resources, Volume 8, issue 1, p 43-81). These results are part of the article "A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae), an endangered migratory Neotropical fish". Scientific Reports, 8: 8511, 2918

Supplementary Data S3: Brycon orbignyanus (Characiformes: Bryconidae) draft partial genome assembly (~10X) in fasta format (.fsa). Assembled from Illumina HiSeq 2000 short reads (retrievable from NCBI-SRA SRX3350440), using SOAPdenovo 2 (k-mer=55) with the intention to screen for microsatellite loci. This assembly A1 was the base for the alignments performed with SOAPaligner retrivable from NCBI-SRA SRX3427716).
The final size of the genomic assembly A1 is 1,113,754,917 bp (including unknown base calls and gaps, N) and 1,039,212,289 bp (not counting Ns – Δ=74,542,628). A total of 1,273,306 contigs or scaffolds were obtained, the shortest being 100 bp and the longest 172,138 bp (average=874). Only 55 scaffolds were longer than 100 kbp; 1.97% longer than 10 kbp; 11% longer than 1 kbps and 18.09% of 500 bp or more. The A1 assembly had the CG content of 41.18% and N50=8,463.
These results are part of the article "A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae), an endangered migratory Neotropical fish". Scientific Reports, 8: 8511, 2918

Supplementary Table S2 - A broad genomic panel with potentially amplifiable microsatellite loci for Brycon orbignyanus is publicly made available. Loci marked with an asterisk (*) have been empirically validated as polymorphic (Arias et al., 2016; Conservation Genetics Resources, Volume 8, issue 1, p 43-81). These results are part of the article "A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae), an endangered migratory Neotropical fish". Scientific Reports, 8: 8511, 2918

Assemblathon 2 is a genome assembly contest where participating teams attempted to assemble genomes for three vertebrate species using a mixture of next-generation sequencing data. In total, 43 assemblies were submitted for three species (15 for bird, 16 for fish, and 12 for snake). These assemblies were assessed using a wide variety of statistical approaches as well as using experimental data from Fosmid sequences and optical maps.