Metagenome Assembly and Curation

Illumina reads that passed quality control were assembled, each sample separately, using megahit v1.1.1 (Liu et al., 2015 (link)) with the parameters (-t 20 -m 0.8 --preset meta-sensitive), whereas 454 reads were assembled using Newbler v.2.9 (Roche) using default parameters, since Newbler has better performance than other assemblers for Roche 454 reads (Kumar and Blaxter, 2010 (link)). Produced contigs were renamed according to the following pattern: freshwater_SRRAccession.contig000XXXXXX, where SRRAccession is the SRA Run accession number of the particular sample used for assembly and XXXXXX is a serial number. Metagenomes that produced no contigs longer than or equal to 1,000 bp were removed from further analysis.