screen usage and readme update

README.md

@@ -183,8 +183,7 @@ You can pass through snakemake options to restrict CPU/memory/cluster resources
 
 ### Filtering common contaminants:
 
-Verkko has the ability to filter common contaminants from an assembly using the `--screen` option. For human samples, you can specify `--screen human` which will automatically filter the mitochonrdia, rDNA, and EBV sequences. For other samples you can specify an arbitrary number of targets using `--screen exampleN exampleN.fasta`. For each contaminant, verkko will remove all sequences matching the target from the main assembly output. It will also identify a 'cannonical' reprentative by coverage and circularize it to remove self-similarity at the start/end.
-
+Verkko has the ability to filter common contaminants from an assembly using the `--screen` option. You can specify an arbitrary number of targets using multiple `--screen <contaminant_N_name> <contaminant_N_sequence.fasta>`  commands. For each contaminant, verkko will remove all sequences matching the target from the main assembly output. It will also identify a ‘canonical’ representative by coverage and circularize it to remove self-similarity at the start/end. For typical contaminants of human assemblies we have special option `--screen-human-contaminants` which requires no parameters and is a shortcut for `--screen rDNA rdna.fasta --screen mitochondria mito.fasta --screen EBV ebv.fasta`.
 ## Outputs:
 The final assembly result is under `asm/assembly.fasta`. The final graph (in homopolymer-compressed space) is under `asm/assembly.homopolymer-compressed.gfa` along with coverage files in `asm/assembly*csv`. There is also an `asm/assembly.scfmap` file which translates the final sequence name in `assembly.fasta` to graph nodes. You can find intermediate graphs and coverage files under `asm/*/unitig-*gfa` and `asm/*/unitig-*csv`.
 

src/verkko.sh

@@ -947,11 +947,9 @@ if [ "x$help" = "xhelp" -o "x$errors" != "x" ] ; then
     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 ""
-    echo "    --screen <option>        Identify common contaminants and remove from the assembly, saving 1 (circularized) exemplar."
-    echo "                             For human, '--screen human' will attempt to remove rDNA, mitochondria, and EBV."
-    echo "                             Arbitrary contaminants are supported by supplying a name and fasta:"
-    echo "                             '--screen contaminant /full/path/to/contaminant.fasta'"
-    echo "                             Multiple screen commands are allowed and are additive."
+    echo "    --screen <contaminant_name> </full/path/to/contaminant.fasta>"
+    echo "                             Screens contaminant from provided file. Multiple screen commands are allowed and are additive."
+    echo "                             To screen typical contaminants of human assemblies one can use --screen-human-contaminants option with no parameters, which removes rDNA, mitochondria and EBV."
     echo ""
     echo "    --paths <gaf paths>      No assembly, generate consensus given paths and an existing assembly."
     echo "                             The gaf file must be formatted as follows: 'name >utig4-1<utig4-2 HAPLOTYPE1'. One per line."