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• Aim 3: Study the construction of diverse communities in soil

  This milestone will require incorporating a few additional databases/annotation tools. For example, KEGG, AntiSMASH and CARD

  No due date

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• Aim 2: Develop pangenome-aware algorithms to leverage co-occurence of the same species in multiple samples

  In this aim we will use multi-sample coverage information to improve individual species assemblies in each sample while constructing annotated pangenomes across the sample set, identify variant haplotypes in individual samples, identify genome rearrangements across samples and compare coverage of individual genes across samples, rather than contigs, in a manner similar to methods used to infer co-expressed genes in transcriptome studies.

  No due date

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• Aim 1: Develop algorithms to leverage taxonomy information and universally-conserved marker genes for binning both well-characterized and divergent species

  In this aim we will develop methods to extract as much information as possible from single metagenomic assemblies to produce high-quality bins and provide the best possible grounding for refinement with multisample information.

  No due date

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