Table 1 List of software in the MetaG, MetaT, MetaP workflows
Workflow | Software version | References/webpage |
|---|---|---|
MetaG | ||
Trimming | Trim Galore! (Galaxy version 0.6.7 + galaxy0) | (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) |
Quality control | FastQC (Galaxy version 0.73 + galaxy0) | (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) |
Assembly | MEGAHIT (Galaxy version 1.1.3.5) | [30] |
Assembly quality | metaQUAST (Galaxy version 5.2.0 + galaxy0) | [31] |
Binning | MaxBin2 (Galaxy version 2.2.7 + galaxy3) | [19] |
Dereplication* | dRep (Galaxy version 3.2.2 + galaxy0) | [32] |
Genome quality assessment | CheckM lineage_wf (Galaxy Version 1.2.0 + galaxy0) | [33] |
Read coverage | CoverM-GENOME (Galaxy Version 0.2.1 + galaxy0) | |
Read coverage | CoverM-CONTIG (Galaxy Version 0.2.1 + galaxy0) | |
Bin annotation | CAT bins (Galaxy version 5.0.3.0) | [34] |
Gene prediction | FragGeneScan (Galaxy version 1.30.0) | [35] |
CAZyme annotation | Hmmscan (Galaxy version 0.1.0) with dbCAN-HMMdb-V10 | |
KOfam annotation | KofamScan (Galaxy version 1.3.0 + galaxy1) | |
Functional annotation | Interproscan (Galaxy version 5.0.0) | [39] |
MetaT | ||
Trimming | Trimmomatic (Galaxy version 0.38.1) | [40] |
Quality control | FastQC (Galaxy version 0.73 + galaxy0 | (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) |
rRNA removal | SortMeRNA (Galaxy version 2.1b.6) | [41] |
mRNA quantification and mapping | Kallisto quant (Galaxy version 0.46.0.4) | [42] |
MetaP | ||
Protein quantification | MaxQuant (Galaxy version 1.6.3.4) | |