Metatranscriptome analysis
Raw data were processed using SqueezeMeta v1.4.0 pipeline (Tamames &
Puente-Sanchez 2019). Assembly was done using Megahit (Li et al 2015).
Short contigs (<150 bps) were removed using prinseq (Schmieder
et al., 2011). Contig statistics were done using prinseq (Schmieder et
al., 2011). RNAs were predicted using Barrnap (Seeman 2014). 16S rRNA
sequences were taxonomically classified using the RDP classifier (Wang
et al., 2007). tRNA/tmRNA sequences were predicted using Aragorn
(Laslett & Canback 2004). ORFs were predicted using Prodigal (Hyatt et
al., 2010). Similarity searches for GenBank (Clark et al 2016), eggNOG
(Huerta-Cepas et al., 2016), KEGG (Kanehisa and Goto, 2000), were done
using Diamond (Buchfink et al., 2015). HMM homology searches were done
by HMMER3 (Eddy, 2009) for the Pfam database (Finn et al., 2016). Read
mapping against contigs was performed using Bowtie2 (Langmead and
Salzberg, 2012). Pathway prediction for KEGG (Kanehisa and Goto, 2000)
and MetaCyc (Caspi et al., 2018, Nucleic Acid Res 46(D1), D633-D639)
databases was done using MinPath (Ye and Doak, 2009).