Update readme.md

readme.md

@@ -8,62 +8,63 @@ Compressed folder "decontaMiner_1.4.tar.gz" contains latest version of the tool.
 
 DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. DecontaMiner builds an offline HTML page containing summary statistics and plots. The software is freely available at http://www-labgtp.na.icar.cnr.it/decontaminer.
 
-## Database download link (Pre built)
+## Three Main scripts to Run
+#### Step 1 :     (a) decontaMiner.sh 
+#### Step 2 :     (b) filterBlastInfo.sh and
+#### Step 3 :     (c) collectInfo.sh
+
+### Database download link (Pre built)
 https://drive.google.com/drive/u/2/folders/1UQCiuUVnS5TpkT0We2AkRVew-km_gR_u
 
-## R script for o/p visualization 
+### R script for o/p visualization 
 
 Please find the code here https://rpubs.com/amarinder1/deontaminer or https://github.com/amarinderthind/decontaminer/tree/master/R_decontaminer_visualizationScript
 
 ### some updates for database configration settings 
 
 if you have fasta and idx path as listed below
 
-###### fasta path        DB/HUMAN_RNA/rRNA.fasta
-###### idx path          DB/HUMAN_RNA/rRNA.idx
+######     fasta path      `    `       DB/HUMAN_RNA/rRNA.fasta
+######     idx path        `    `       DB/HUMAN_RNA/rRNA.idx
 
 You should mention this in configuration file in the following way 
-
-##### RIBO_DB=DB/HUMAN_RNA
-##### RIBO_NAME=rRNA
-
-## Download link for example BAM files
+```
+RIBO_DB=DB/HUMAN_RNA
+RIBO_NAME=rRNA
+```
+### Download link for example BAM files
 https://drive.google.com/drive/u/2/folders/1B9WNJc1cGY_LIi2XGwkQ0h_9916_A8Ij 
 
-## Three Main scripts to Run
-#### (a) decontaMiner.sh 
-#### (b) filterBlastInfo.sh and
-#### (c) collectInfo.sh
 
 ### Updates on Paired end reads error
 
-
-```
 Decontaminer expects the following Paired end reads format:
 
+```
 @A00121:137:HTLF3DSXX:3:1110:3097:35571/1
 @A00121:137:HTLF3DSXX:3:1110:3097:35571/2
-
+```
 If you have other reads format (like below) format of PR reads, you can rename/change from 
 
+```
 @A00121:137:HTLF3DSXX:3:1110:3097:35571 0:N: 00
 @A00121:137:HTLF3DSXX:3:1110:3097:35571 1:N: 00
-
+```
 To following using simple linux command (mentioned below), with this command it will be converted to the required format like below:
-
+```
 @A00121:137:HTLF3DSXX:3:1110:3097:35571/1
 @A00121:137:HTLF3DSXX:3:1110:3097:35571/2
-
+```
 Here is an example of Linux command 
-
+```
 sed 's/ 0:N:0://1/g' inputfile > outputfile
 sed 's/ 1:N:0://2/g' inputfile > outputfile
 ```
 
-### 
+## Flow Chart of the Pipeline
 
 ![Image of Decontaminer PipeLine](https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12859-019-2684-x/MediaObjects/12859_2019_2684_Fig1_HTML.png?as=webp)
 
-### Overview of the results
+## Overview of the results Visualization 
 
 ![Image of Decontaminer PipeLine](https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12859-019-2684-x/MediaObjects/12859_2019_2684_Fig5_HTML.png?as=webp)