Multi-omics highlights challenges in assessing the composition and performance of microbial consortia for commercial applications

Supplementary data and code for "Multi-omics highlights challenges in assessing the composition and performance of microbial consortia for commercial applications".

rRNAProbesandFasta.zip contains the rRNA sequences covering a substantial proportion of rRNA undepleted by Ribo-Zero Plus and the generated probe sequences from these sequences for synthesis for supplementary depletion.

The combined 98 MAGs from short- and long-reads discussed in the manuscript are available in 98_MAGs.tar.gz.

SqueezeExtBins.zip and SqueezeCoassemblyNF.zip contain the sqm2zip outputs for an external bins provided analysis (98_MAGs.tar.gz) and the complete SqueezeMeta workflow using coassembly on the DNA and RNA short read datasets generated. These files can be imported via SQMtools for analysis.

Ribosomal rRNA after RiboZeroPlus depletions is provided in:

NitrifyingRNA_Day0_RiboZeroPlusKit_combinedribo_R1.fastq.gz

NitrifyingRNA_Day0_RiboZeroPlusKit_combinedribo_R2.fastq.gz

The MAGs used in the supplemental rRNA probe design are in: 

SupplementalProbe_MAGs.zip

The unaligned rRNA reads not matching the above MAGs are in:

unaligned_reads.1.fastq.gz

unaligned_reads.2.fastq.gz

Additional details are available at: https://github.com/carleton-envbiotech/Consortium_meta_omics/

BioProject with SRA deposit for raw data available at: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1165788