Updates README.md with details on how FMindexing removes artificially…

… generated sequences.

Former-commit-id: ecfc3d3

README.md

@@ -44,15 +44,19 @@ ggCaller can take a list of fasta files (one file per line), or a Bifrost GFA fi
 
 To run ggCaller from the command line, pass arguments specifying input/output and parameters for traversal.
 
+ggCaller additionally employs FMindexing to remove artificial sequences generated by incorrectly phased nodes in the DBG. This is only employed when the input sequences are exclusively assembled genomes. 
+
 #### If Bifrost GFA and Colours file already exist:
 
 To run ggCaller using an existing Bifrost GFA file and Colours file, specify BOTH:
 - ```--graph <graph.gfa>``` Input GFA
 - ```--colours <colours.bfg_colors>``` Input colours file
 
-Note: Ensure the sequences used to build the graph are in the same directories as when the graph was built. If the sequences you used to generate the GFA and Colours files were exclusively assembled genomes, additionally specify:
+To enable filtering of artificially generated sequences via FMindexing (if sequences used to generate the GFA and Colours files were exclusively assembled genomes), additionally specify:
 - ```--is-ref```
 
+Note: Ensure the sequences used to build the graph are in the same directories as when the graph was built.
+
 #### If Bifrost GFA and Colours file do not exist:
 
 To build a new Bifrost graph using assembled genomes and/or reads, specify ONE OR BOTH: