Output

Tables

Tables are given in CSV format and are ready-to-use for downstream analysis. They can be found in the {OUTDIR}/tables directory.

Example table: Relative abundance of CAZymes found in termite guts.

sample	cazyme	tpm	num_reads
A_dentosus_BEC331	GH13_39	3363.395428	30
A_heterognathus_BEC338	GH4	2547.609582	9
A_heterognathus_BEC338	GH3	1923.279398	6
A_heterognathus_BEC338	GH24	1585.993103	9
A_heterognathus_BEC338	GH25	1094.34099	19
A_heterognathus_BEC338	CE11	1172.859369	34
A_heterognathus_BEC338	GT2_Glyco_tranf_2_5	6526.699973	20
A_heterognathus_BEC338	GH42	1196.700335	59
A_heterognathus_BEC338	GH13_9	626.776231	26
A_heterognathus_BEC338	GT35	1641.945607	31
A_heterognathus_BEC338	GT35	1981.665284	5
A_heterognathus_BEC338	GH116	808.882501	28
A_heterognathus_BEC338	GH3	984.358566	72
A_heterognathus_BEC338	PL12_3	1066.674473	65
A_heterognathus_BEC338	GH13_39	2484.017659	4
A_heterognathus_BEC338	GT11	1248.473785	25
A_heterognathus_BEC338	GT2_Glycos_transf_2	2070.79998	19
A_heterognathus_BEC338	GH5_4	1264.794929	24
A_heterognathus_BEC338	GH13_20	1396.864788	71
A_laurensis_BEC8	GT84	1167.127621	37
A_laurensis_BEC8	GH5_4	1210.464931	35
A_laurensis_BEC8	GH177	2181.267745	35
A_laurensis_BEC8	GH13_39	1183.980398	23
A_obeuntis_BEC335	GH51_1	1017.639248	17
A_obeuntis_BEC335	GT104	1014.976659	21
A_obeuntis_BEC335	GH9	1216.003067	12
A_obeuntis_BEC335	GH5_36	1216.003067	12
…	…	…	…

Figures

Figures are given in PDF and HTML format and are publication-ready. They can be found in the {OUTDIR}/figures directory.

Example PDF Presence/absence of metabolic pathway genes involved in lignocellulose digestion found in MAGs (metagenome-assembled genomes). Completeness and contamination of MAGs is given on the left site; lighter colours indicate higher completeness and less contamination, respectively. Purple squares indicate absence of genes and yellow squares indicate presence of genes. Note that some genes are shared between pathways, for instance genes of the Rnf complex.

Download here an example HTML file