Outputs
Results are stored in the output folder (default 'mercat_results' of the current working directory)
- The 'report' folder contains an html report with interactive plotly figures
- If at least 4 samples are provided a PCA plot will be included in the html report
- The 'tsv' folder contains counts tables in tab separated format
- If protein files are given, or the
-prodoption, a .tsv file is created for each sample containing k-mer count, pI, Molecular Weight, and Hydrophobicity metrics - If nucleotide files are given a .tsv file is created for each sample containing k-mer count and GC content
- If protein files are given, or the
- If .fastq raw reads files are used, a 'clean' folder is created with the clean fasta file.
- If the
-prodoption is used, a 'prodigal' folder is created with the amino acid .faa and .gff files - If the
-fgsoption is used, a 'fgs' folder is created with the amino acid .faa file
Alpha and Beta diversity metrics provided by MerCat2 are experimental. We are currently working on the robustness of these measures.
| Alpha diversity metrics provided | Beta diversity metrics provided |
|---|---|
| shannon | euclidean |
| simpson | cityblock |
| simpson_e | braycurtis |
| goods_coverage | canberra |
| fisher_alpha | chebyshev |
| dominance | correlation |
| chao1 | cosine |
| chao1_ci | dice |
| ace | hamming. |
| jaccard | |
| mahalanobis | |
| manhattan (same as City Block in this case) | |
| matching | |
| minkowski | |
| rogerstanimoto | |
| russellrao | |
| seuclidean | |
| sokalmichener | |
| sokalsneath | |
| sqeuclidean | |
| yule |