Some cleaning

Author: lenak01

DuWTill/README.md

@@ -1,15 +1,15 @@
 # DuWTill data and configuration 
 ## Blast portal
-Local BLAST+ is freely available from National Center for Biotechnology Information (NCBI). Download the self-extracting archive `ncbi-blast-2.#.#+-win64.exe` for your desired version from [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+). We tested the database on versions 2.6.0 and 2.7.1. Detailed instruction on installation can be found [here](https://www.ncbi.nlm.nih.gov/books/NBK52637/). Namely,
+Local BLAST+ is freely available from National Center for Biotechnology Information (NCBI). Download the self-extracting archive `ncbi-blast-2.#.#+-win64.exe` for your desired version from [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+). We tested the database on versions 2.6.0 and 2.7.1. Detailed instructions on the installation can be found [here](https://www.ncbi.nlm.nih.gov/books/NBK52637/). Namely,
 >The BLAST+ archive ... contains a built-in installer. Accepting the license agreement after double-clicking, the installer will prompt for an installation directory. ... Clicking the "Install" button, the installer will create this directory with a "doc" subdirectory containing a link to the BLAST+ user manual, an "uninstaller" for future removal of the installation, and a "bin" subdirectory where the BLAST programs and accessory utilities are kept.
 
 Setting environment variables is not compulsory.
 
-**Note:** this install must be outside of IIS; we recommend neutral `C:\blast-2.7.1+` (in our case).
+**Note:** this install must be outside of IIS; we recommend the neutral directory `C:\blast-2.7.1+` (in our case).
 ## DECaR
 1. In addition to the above create two folders `db` and `temp` in the BLAST directory (`C:\blast-2.7.1+`).
 2. Download DECaR reference from https://adelaide.figshare.com/... and unzip it into `C:\blast-2.7.1\db\DECaR.fa`
-3. Prepare reference database. From a command prompt execute:
+3. Prepare the reference database. From a command prompt execute:
 ```bash
 cd C:\blast-2.7.1+
 bin\makeblastdb -in db\DECaR.fa -dbtype nucl -out db\DECaR -title "Durum Exome Capture Reference (DECaR)"
@@ -26,4 +26,4 @@ bin\makeblastdb -in db\DECaR.fa -dbtype nucl -out db\DECaR -title "Durum Exome C
     ...
 ```
 ## Mutations
-SQLite database of called mutations Tilling.sqlite is supplied with DuWTill project in App_Data folder. There is no need to change third key in `appSettings` (see above) unless you are substituting your own data. In that case please refer to README in YouDB project.
+The SQLite database of called mutations Tilling.sqlite is supplied with the DuWTill project in the App_Data folder. There is no need to change the third key in `appSettings` (see above) unless you are substituting your own data. In that case please refer to README in the YouDB project.

README.md

@@ -1,5 +1,5 @@
 # DuWTill 
-DuWTill is a simple Web client to the database of mutations in the South Australian Durum Wheat Tilling (DuWTill) collection created as part of a joint project between Australian Centre for Plant Functional Genomics (ACPFG), University of Saskatchewan and Università degli Studi della Tuscia for the project “A Molecular Diversity Drive for Precision-Engineered Wheat”.
+DuWTill is a simple Web client for the database of mutations in the South Australian Durum Wheat Tilling (DuWTill) collection created as part of a joint project between Australian Centre for Plant Functional Genomics (ACPFG), University of Saskatchewan and Università degli Studi della Tuscia for the project “A Molecular Diversity Drive for Precision-Engineered Wheat”.
 
 ## Data content
 Seeds of an advanced durum breeding line, UAD0951096_F2:5 (which has given rise to the commercially grown cultivar DBA-Aurora), were mutagenized with 0.7% EMS and 500 mutant plants were grown through one further generation to seed. In the next generation (M2) DNA from 100 of these plants and the unmutagenized control (UAD0951096_F2:5) were sequenced (Illumina, 2x150 bp) following reduction by exome capture using the 106.9 Mb [Roche NimbleGen SeqCap](https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/shareddesigns.html) Wheat Exome Design. 
@@ -9,20 +9,20 @@ To improve variant calling, a novel consolidated Durum Exome Capture Reference (
 Reads of the 100 exome-captured samples were aligned to DECaR. Any variation from DECaR was considered a mutation if it was present in only one mutant sample and non-polymorphic between the control and DECaR. We also demanded a mutation to be covered by at least three reads, and had sufficient coverage for the control allele in at least 50 other mutant samples. DECaR also allowed us to predict zygosity of the mutations discovered.
 
 For further details and to cite:
->Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis J. Pozniak, Penny J. Tricker, Ute Baumann "Novel Informatics Tools to Support Functional Annotation of the durum wheat genome." (In review)
+>Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis J. Pozniak, Penny J. Tricker, Ute Baumann "Novel Informatics Tools to Support Functional Annotation of the durum wheat genome." Frontiers in Plant Science (In review)
 
 ## DuWTill Web Server
 The identified mutations are accessible on a public DuWTill Web server http://duwtill.acpfg.com.au.
 
 ## Local Build (Windows)
-We included two projects in this distribution: DuWTill itself and YourDB console application, handy if you want to investigate your own data. **For further instructions, please refer a README in each project**.
+We included two projects in this distribution: DuWTill itself and the YourDB console application, which is useful if you want to investigate your own data. **For further instructions, please refer a README in each project**.
 ### Prerequisites
-1. **Internet Information Services (IIS)**. Turn this Windows feature on from the `Control Panel->Turn Windows features on or off`. There is a good instruction on how to do it [here](https://www.howtogeek.com/112455/how-to-install-iis-8-on-windows-8/). We used IIS 8.0 Express for development and IIS 10.0 on DuWTill Web server. 
+1. **Internet Information Services (IIS)**. Turn this Windows feature on from here: `Control Panel->Turn Windows features on or off`. There are good instructions on how to do it [here](https://www.howtogeek.com/112455/how-to-install-iis-8-on-windows-8/). We used IIS 8.0 Express for development and IIS 10.0 on DuWTill Web server. 
 2. **Visual Studio 2015 or later**, downloadable from the [official Web site](https://visualstudio.microsoft.com/vs/older-downloads/).
 ### Build
-1. Download and unzip the [DuWTill release](https://github.com/CroBiAd/DuWTill/releases).
+1. Download and unzip the [DuWTill release](https://github.com/CroBiAd/DuWTill/releases/latest).
 2. Open the `WebTilling.sln` file in Visual Studio. 
-3. Follow the instruction in README in each project
+3. Follow the instruction in README in each project.
 4. Build the solution.
 
-These steps should resolve dependencies and download required packages. You are ready to publish the application to IIS.
+These steps should resolve dependencies and download the required packages. You are then ready to publish the application to IIS.

YourDB/README.md

@@ -1,9 +1,9 @@
 # YourDB
-This project's sole purpose is to help with formatting mutations calls as an SQLite database.
-* If you have no intent to substitute you own data, don't read further. Our mutations calls are already in App_Data folder of DuWTill project.
-* If you prefer other means of creating SQLite database, say [Mozilla add-on](https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager-webext/), do it. But refer to the table description below and in Program.cs.
+This project's sole purpose is to help with formatting mutation calls as an SQLite database.
+* If you have no intent to substitute you own data, don't read further. Our mutation calls are already in the App_Data folder of the DuWTill project.
+* If you prefer other means of creating the SQLite database, say [Mozilla add-on](https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager-webext/), do it. But refer to the table description below and in Program.cs.
 * If you want to switch to SQL Server, you can do it too with the appropriate **solution configuration** (not discussed here as part of this distribution). We tried SQLExpress and full blown SQL Server.
-* If you need to substitute the reference as well, follow the instructions in README in DuWTill project on how to create blastable database.
+* If you need to substitute the reference as well, follow the instructions in README in the DuWTill project on how to create a blastable database.
 
 We presume that you've called mutations by following our [pipeline](https://github.com/CroBiAd/TILLinG-mutants) or by other means. Then,
 
@@ -21,8 +21,8 @@ We presume that you've called mutations by following our [pipeline](https://gith
    * *chr*	- chromosome of the sequence containing the mutation
    * *flankStart*	- start of a flanking sequence
    * *flankEnd* - end of a flanking sequence
-   * *assemblyID* - optional, we kept original naming from Svevo and Kronos assemblies
-2. **YourDB** is a simple console application which is better to run from within Visual Studio. Copy csv file described above into `DuWTill\App_Data` folder and set command line arguments and working directory on `YourDB->Properties->Debug` page, if required:
+   * *assemblyID* - optional, we kept original naming from the Svevo and Kronos assemblies
+2. **YourDB** is a simple console application which is better to run from within Visual Studio. Copy the csv file described above into the `DuWTill\App_Data` folder and set the command line arguments and working directory on the `YourDB->Properties->Debug` page, if required:
 
    ![alt text](debug.png "Command line arguments on Debug page")
 
@@ -34,7 +34,7 @@ We presume that you've called mutations by following our [pipeline](https://gith
 
    Program accepts short/long Linux/Windows styles, i.e. `--csvfilename=Tilling` OR `-f=Tilling` OR `/csvfilename:Tilling` OR `/f:Tilling`
 
-3. You can now run YourDB (Ctrl+F5). The results would be similar to 
+3. You can now run YourDB (Ctrl+F5). The results will be similar to this: 
 
    ![alt text](run.png "Example output from YourDB")