Update README.md

README.md

@@ -13,28 +13,28 @@ Winnowmap requires C++ compiler with c++11 and openmp, which are available by de
 	cd Winnowmap
 	make -j8
   ```
-Expect `winnowmap` and `meryl` executables in `bin` folder. The `recursive` option used above is necessary to download all submodules .
+Expect `winnowmap` and `meryl` executables in `bin` folder.
 
 ## Usage
 
 For either mapping long reads or computing whole-genome alignments, Winnowmap requires pre-computing high frequency k-mers (e.g., top 0.02% most frequent) in a reference. Winnowmap uses [meryl](https://github.com/marbl/meryl) k-mer counting tool for this purpose.  
 
-*  Mapping ONT or PacBio WGS reads
+*  Mapping ONT or PacBio-hifi WGS reads
   ```sh
-	meryl count k=15 output merylK15 ref.fa
-	meryl print greater-than distinct=0.9998 merylK15 > repetitiveK15.txt
+	meryl count k=15 output merylDB ref.fa
+	meryl print greater-than distinct=0.9998 merylDB > repetitive_k15.txt
 
-	winnowmap -W repetitiveK15.txt -t 36 -ax map-ont ref.fa ont.fq.gz > output.sam  [OR]
-	winnowmap -W repetitiveK15.txt -t 36 -ax map-pb ref.fa hifi.fq.gz > output.sam
+	winnowmap -W repetitive_k15.txt -t 36 -ax map-ont ref.fa ont.fq.gz > output.sam  [OR]
+	winnowmap -W repetitive_k15.txt -t 36 -ax map-pb ref.fa hifi.fq.gz > output.sam
   ```
 
 *  Mapping genome assemblies
 
   ```sh
-	meryl count k=19 output merylK19 asm1.fa
-	meryl print greater-than distinct=0.9998 merylK19 > repetitiveK19.txt
+	meryl count k=19 output merylDB asm1.fa
+	meryl print greater-than distinct=0.9998 merylDB > repetitive_k19.txt
 
-	winnowmap -W repetitiveK19.txt -t 36 -ax asm20 asm1.fa asm2.fa > output.sam
+	winnowmap -W repetitive_k19.txt -t 36 -ax asm20 asm1.fa asm2.fa > output.sam
   ```
   Adjust the thread count `-t` based on your CPU. For the genome-to-genome use case, it may be useful to visualize the dot plot. This [perl script](https://github.com/marbl/MashMap/blob/master/scripts) can be used to generate a dot plot from [paf](https://github.com/lh3/miniasm/blob/master/PAF.md)-formatted output. In both usage cases, pre-computing repetitive k-mers using [meryl](https://github.com/marbl/meryl) is quite fast, e.g., it typically takes 2-3 minutes for the human genome reference.