Merge branch 'main' of https://github.com/ViralVerity/DENV_pipeline

merge

README.md

@@ -2,17 +2,18 @@
 
 Created by Verity Hill and Chrispin Chaguza, Grubaugh Lab
 
-Still a bit beta - please feel free to have a go and report any issues you get! Please provide a screenshot of the error and all log files produced so that I can see what's gone wrong.
-
-**This pipeline is still in active development including argument names and input files. Use ```git pull``` and reinstall using ```pip install .``` every time you run it**
-
-This pipeline takes raw read data in the form of fastq files, maps them against provided bed files and then provides a series of outputs for further analysis including consensus sequences. 
+This pipeline takes raw Illumina read data in the form of fastq files, maps them against provided bed files and then provides a series of outputs for further analysis including consensus sequences. 
+The following pipeline works with ONT data: https://github.com/josephfauver/DENV_MinION_Script
 
 IMPORTANT: the bed files must correspond to the wet lab protocol that you used and the reference sequence used to generate them otherwise the sequences generated will be incorrect. 
 
 It calls input files as a virus type if it has more than 50% coverage of the reference genome provided.
 
-If running on a server, it is highly recommended to run using screen/tmux or similar.
+If running on a server, it is highly recommended to run it using screen/tmux or similar.
+
+# Tips
+
+- make sure that there are no dots in the reference name
 
 # Installation instructions