Computational protocol: Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation

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Protocol publication

[…] All sequence reads were used for similarity searches against the NR database, employing the program RAPsearch2 [] with an E value cutoff of 0.001. Based on the results of these searches, taxonomy assignment was made using MEGAN5 [] using default parameters (minScore = 50.0, maxExpected = '0.01', topPercent = 10.0, minSupport = 50, minComplexity = 0.44). Analysis of the abundance of microbial pathways was performed with HUMAnN software [] on the basis of the results of another RAPSearch2 run with all reads, using an Evalue of 0.001 as the threshold. The reference database consisted of proteomes of the major Archaeal species identified by MEGAN5 (if available) and selected high quality proteomes obtained from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [] as suggested by the HUMAnN developers. Metagenome assembly was performed with MetaVelvet version 1.1 using a maximal kmer length of 31 and automated peak detection []. Assembled contigs were mapped to bacterial and archaeal genomes from the NCBI database using the BWA MEM algorithm []. […]

Pipeline specifications

Software tools RAPSearch, MEGAN, HUMAnN, MetaVelvet, BWA
Application Metagenomic sequencing analysis
Organisms Beta vulgaris subsp. vulgaris, Dipturus trachyderma
Chemicals Hydrogen, Methane