DOC: Explain output to fix #36

metagentools · Jul 26, 2023 · 2cb65c7 · 2cb65c7
1 parent 9cb0a03
commit 2cb65c7
Showing 1 changed file with 11 additions and 1 deletion.
diff --git a/docs/usage.md b/docs/usage.md
@@ -98,4 +98,14 @@ metacoag --assembler megahit --graph /path/to/graph_file.gfa --contigs /path/to/
 
 ```
 metacoag --assembler flye --graph /path/to/assembly_graph.gfa --contigs /path/to/assembly.fasta --paths /path/to/assembly_info.txt --abundance /path/to/abundance.tsv --output /path/to/output_folder
-```
+```
+
+# Output
+
+The output of MetaCoAG will contain the following main files and folders.
+
+* `contig_to_bin.tsv` containing the comma separated records of `contig id, bin number`
+* `bins` containing the identified bins (FASTA file for each bin)
+* `low_quality_bins` containing the identified low-quality bins, i.e., having lower than `bin_mg_threshold` fraction of marker genes (FASTA file for each bin)
+* `*.frag.faa`, `*.frag.ffn` and `*.frag.gff` files containing FragGeneScan output
+* `*.hmmout` containing HMMER output