In addition, the broader genomic context of interesting features may be further elucidated by sorting (or “binning”) partially assembled genome fragments into categories (so-called “bins”). The aim of this approach is to separate fragments that likely originate from different species while grouping those together that likely belong to the same species, leading to partial or even complete reconstruction of genomes from metagenomic datasets. The range of available metagenomic binning tools is very diverse [16–19] and newer approaches in binning algorithms even allow the sorting of sequence fragments of unassembled reads [20,21], if sufficient read length and quality is provided. The reliability and efficiency of metagenome binning however increases substantially with longer sequence fragments. Therefore, regardless of whether the research goal is to elucidate the taxonomic and metabolic diversity a microbial community, or to attempt the genome reconstruction of individual community members, metagenome assemblies are a crucial step for greatly enhancing subsequent analyses.

二，宏基因组装软件

三，软件挑战赛
https://www.microbiome-cosi.org/
https://data.cami-challenge.org/
Challenges
CAMI II offers several challenges: an assembly, a genome binning, a taxonomic binning and a taxonomic profiling challenge, on several multi-sample data sets from different environments, including long and short read data. This includes a marine data set, a high-strain diversity data set, and a rhizosphere data set. A pathogen detection challenge on a clinical sample is also offered.

Assembly challenge: takes as input read samples of a given data set, and returns a cross-sample assembly or single sample assemblies. Assembly results can be submitted for short read data OR long read data, OR both data types combined. For methods incapable of submitting a cross-sample assembly for the entire data set, the FIRST TEN samples of a data set can be assembled and a ten-sample cross-assembly submitted. Participants can also submit single-sample assemblies for each of the first five samples of a data set. The assembly challenge will close early, namely once a gold standard assembly has been released after 4.5 months! Details of the specifications of the CAMI evaulation for strain-aware assemblers can be found at https://www.microbiome-cosi.org/images/Specification_of_CAMI_evaluation_for_strain-aware_assemblers.pdf

Profiling challenge: takes as input multiple read samples of a given data set and returns taxonomic profiles for all individual samples and one for the entire data set. This challenge closes after the second challenge period has ended.

Genome binning challenge: takes as input reads, or gold standard assemblies, or assemblies provided by CAMI after three months for every sample individually. It returns genome bin assignment for the analysed reads or contigs for every sample of a data set in the CAMI format.

Taxon binning challenge: takes as input reads, or gold standard assemblies, or assemblies provided by CAMI after three months. It returns a taxon bin assignment for the analysed reads or contigs in CAMI format for every sample in a data set.

Clinical pathogen detection challenge

Case description: A 32-year-old woman presented to an Emergency Center on March 22nd 2018 because of vomiting, abdominal pain and strong nosebleeds. She claimed to feel well until 5 days prior to admission when she began to develop fever, joint pain and muscle pain. Four days before admission she presented to her general practitioner and was diagnosed with influenza-like illness. One day before admission, her state rapidly deteriorated with onset of intense abdominal pain, followed by vomiting and nosebleeds, prompting her to present to the Emergency Center. She was never hospitalized for any medical illness. She denied any recent trauma. Four days prior to onset of symptoms, she had returned from a one-month hiking trip between Fethiye and Antalya in Turkey. She denied any unusual contact with wildlife or eating raw meats during her trip. The hospital has sent you a nasal swab for sequencing in order to identify the causative agent. You have generated a paired-end MiSeq sequence sample from this for further analysis.The results of classical molecular tests are still pending.
参考：
1，https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169662
2，https://www.nature.com/articles/nmeth.4458.epdf?author_access_token=sZ3LewLUA5C8WKyQk4MwVtRgN0jAjWel9jnR3ZoTv0PgB6HdyfB_ceU59Q9lL-nu2voPXiXceni4NsQibQ8Mf0SaqGvEoYGzT7JzDBlXtR8y3mAulkrcvDVM33y57_9I