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README.md

@@ -40,27 +40,23 @@ frame:    3      2          1      2       1
 ```bash
 
 # install the script:
+
 git clone https://github.com/jonas-fuchs/viral_orf_finder
 cd viral_orf_finder
 
 # run the script:
+
 python3 orf_finder.py infile.fasta > outfile.tabular
 
 # optional arguments:
--r/--reference
-# reference genebank file
--m/--min-length
-# min length of the orfs to find
--i/--internal
-# True/False if script should search for internal orfs
--c/--circular
-# True/False if script should search for circular orfs
--p/--partial
-# True/False if script should search for partial orfs with no START and/or STOP
--n/--no-overlap
-# True/False if script should consider only orfs that do not overlap
--s/--strands
-# + and/or - (+ = positive strand, - = negative strand)
+
+-r/--reference # reference genebank file
+-m/--min-length # min length of the orfs to find
+-i/--internal # True/False if script should search for internal orfs
+-c/--circular # True/False if script should search for circular orfs
+-p/--partial # True/False if script should search for partial orfs with no START and/or STOP
+-n/--no-overlap # True/False if script should consider only orfs that do not overlap
+-s/--strands # + and/or - (+ = positive strand, - = negative strand)
 ```
 
 ### Side note: