add hmms to readme

README.md

@@ -274,6 +274,27 @@ dbxrefs | `<empty>`, `db:id`, `,` separated list  | `VFDB:VF0511`
 
 Protein sequences provided in short Fasta or GenBank format are searched with default thresholds of 90%, 80% and 80% for minimal identity, query and subject coverage, respectively.
 
+#### User-provided HMMs
+
+Bakta accepts user-provided trusted HMMs via `--hmms` in HMMER's text format. If set, Bakta will adhere to the *trusted cutoff* specified in the HMM header. In addition, a max. evalue threshold of 1e-6 is applied. By default, Bakta used the HMM description line as a product description. Further information can be provided via the HMM description line using the *short* format as explained above.
+
+```bash
+# default
+HMMER3/f [3.1b2 | February 2015]
+NAME  id
+ACC   id
+DESC  product
+LENG  435
+TC    600 600
+
+# short
+NAME  id
+ACC   id
+DESC  gene~~~product~~~dbxrefs
+LENG  435
+TC    600 600
+```
+
 ### Output
 
 Annotation results are provided in standard bioinformatics file formats:
@@ -389,6 +410,7 @@ Annotation:
                         Replicon information table (tsv/csv)
   --regions REGIONS     Path to pre-annotated regions in GFF3 or Genbank format (regions only, no functional annotations).
   --proteins PROTEINS   Fasta file of trusted protein sequences for CDS annotation
+  --hmms HMMS           HMM file of trusted hidden markov models in HMMER format for CDS annotation
   --meta                Run in metagenome mode. This only affects CDS prediction.
 
 Workflow: