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Project: Functional genetic diversity of carbon cycling microbes in soils through captured metagenomics

• design of probes, in total 120476 probes targeting extracellular enzymes in C-cycle
  
• we have 90 samples/metagenomes
  
• sequencing on one lane on the Illumina HiSeq 4000 system in paired-end mode (2X150bp)
  
• all metagenomes were submitted to MG-RAST online tool
  
• forward and reverse reads were merged with PEAR, the average length is 196bp
  
• merged sequencing reads were aligned against the custom protein reference database, that was used for the design of oligonucleotide probes, with DIAMOND algorithm
  
• matrix for all samples and families was generated, following parameters were used: identity:60%, average alignment length: 50 (read length is 196), E-value=1e-10
  
• additionally, eggNOG-mapper was used on all merged reads to obtain taxonomic and functional annotations (output files are in Uppmax)