ref to readme

README.md

@@ -126,7 +126,7 @@ To run in PoreC mode, reads should be provided using the --porec option. For exa
       --nano ont/*.fastq.gz \
       --porec porec/*fastq.gz
 
-Hi-C/PoreC integration was tested mostly on human and primate genomes. Please see the --rdna-scaff-ref, --rdna-tangle, --uneven-depth and --haplo-divergence options if you want to assemble something distant from human and/or have uneven coverage. If you encounter issues or have questions about appropriate parameters, please open an [issue](https://github.com/marbl/verkko/issues).
+Hi-C/PoreC integration was tested mostly on human and primate genomes. Please see  --rdna-tangle, --uneven-depth and --haplo-divergence options if you want to assemble something distant from human and/or have uneven coverage. If you encounter issues or have questions about appropriate parameters, please open an [issue](https://github.com/marbl/verkko/issues).
 
 ### Running on a grid
 By default, verkko will run the snakemake workflow and all compute on the local machine. Support for SGE, Slurm LSF, and PBS (untested) can be enabled with options `--grid`. This will run the snakemake workflow on the local machine but submit all compute to the grid. To launch the both the snakemake workflow and compute on the grid, wrap the verkko command in a shell script and submit using your scheduler. If you're using conda, you may need to make the conda-installed python your default. You can do this with the `--python` option when calling verkko

src/verkko.sh

@@ -865,13 +865,15 @@ if [ "x$help" = "xhelp" -o "x$errors" != "x" ] ; then
     echo "                             uncompressed or gzip/bzip2/xz compressed.  Any"
     echo "                             number of files can be supplied; *.gz works."
     echo ""
-    echo "   --porec <files>           List of files containing Pore-C reads."
+    echo "    --porec <files>          List of files containing Pore-C reads."
     echo "                             Input reads can be any combination of FASTA/FASTQ/SAM/BAM,"
     echo "                             uncompressed or gzip/bzip2/xz compressed.  Any"
     echo "                             number of files can be supplied; *.gz works."
+    echo ""
     echo "    --no-rdna-tangle         Switch off option that helps to proceed large rDNA tangles which may connect multiple chromosomes."
     echo "    --telomere-motif         Switch to user-supplied telomere motif, automatically searched in fwd/revcomp version."
     echo "                             By default, the cannonical vertebrate 'CCCTAA' motif is used during Hi-C scaffolding."
+    echo "    --ref <path>             Path to optional reference. It is used only as a guidance during scaffolding."
     echo "    --uneven-depth           Disable coverage-based heuristics in homozygous nodes detection for Hi-C/PoreC phasing."
     echo "    --haplo-divergence       Estimation on maximum divergence between haplotypes, is used only with Hi-C/PoreC data. Should be increased for species with divergence significantly higher than in human. Default: 0.05, min 0, max 0.2"
     echo ""