readme update

README.md

@@ -1,4 +1,3 @@
-
 <img src="./img/logo.png" width="150">
 
 ## Introduction
@@ -9,92 +8,87 @@
 
 # Dependancies
 
-- [Conda](https://conda.io/miniconda.html)  
+-   [Conda](https://conda.io/miniconda.html)  
 
 # Quick start
-Assuming you already have all databases and the conda environment installed
 
-```
-conda activate organdiet
-nextflow run maxibor/organdiet --reads '*_R{1,2}.fastq.gz' -with-report run_report.html -with-dag flowchart.png
-```
+Assuming you already have all databases and the conda environment installed
 
+    conda activate organdiet
+    nextflow run maxibor/organdiet --reads '*_R{1,2}.fastq.gz' -with-report run_report.html -with-dag flowchart.png
 
 # Installation
 
+### 1. Set up conda environments
 
+    wget https://github.com/maxibor/organdiet/archive/v0.2.2.zip
+    unzip v0.2.2.zip
+    cd organdiet-0.2.2
+    conda env create -f envs/organdiet.yml
+    source activate organdiet
 
-### 1. Set up conda environments
-```
-wget https://github.com/maxibor/organdiet/archive/v0.2.2.zip
-unzip v0.2.2.zip
-cd organdiet-0.2.2
-conda env create -f envs/organdiet.yml
-source activate organdiet
-```
 ### 2. Set up Taxonomy database
 
-- Install taxonomy database: `./bin/basta taxonomy -o ./taxonomy`
+-   Install taxonomy database: `./bin/basta taxonomy -o ./taxonomy`
 
 ### 3. Download the Bowtie2 index for the host genome
+
 From [illumina **iGenomes**](https://support.illumina.com/sequencing/sequencing_software/igenome.html)
 
-```
-mkdir hs_genome
-cd hs_genome
-wget ftp://igenome:[email protected]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz
-tar -xvzf Homo_sapiens_Ensembl_GRCh37.tar.gz
-cd ..
-```
+    mkdir hs_genome
+    cd hs_genome
+    wget ftp://igenome:[email protected]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz
+    tar -xvzf Homo_sapiens_Ensembl_GRCh37.tar.gz
+    cd ..
 
 ### 4. Download the organellome database and build Bowtie2 index
+
 From NCBI [Refseq organelles genomes](https://www.ncbi.nlm.nih.gov/genome/organelle/)
-```
-./bin/download_organellome_db.sh
-bowtie2-build organellome_db/organellome.fa organellome_db/organellome
-```
 
+    ./bin/download_organellome_db.sh
+    bowtie2-build organellome_db/organellome.fa organellome_db/organellome
 
-### 4. Case 1: You plan on using the nr database
+### 4. nt/nr database set up: two solutions
 
-#### 4.1.1 Set up `nr` database for [Diamond](https://github.com/bbuchfink/diamond)
-```
-mkdir nr_diamond_db
-cd nr_diamond_db
-wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
-gunzip nr.gz
-mv nr nr.fa
-diamond makedb --in nr.fa -d nr
-cd ..
-```
+#### Case 1: You plan on using the nr database
 
-### 4..1.1 Set up TaxID mapping database
+##### 4.1.1 Set up `nr` database for [Diamond](https://github.com/bbuchfink/diamond)
 
+    mkdir nr_diamond_db
+    cd nr_diamond_db
+    wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
+    gunzip nr.gz
+    mv nr nr.fa
+    diamond makedb --in nr.fa -d nr
+    cd ..
 
-- Install *prot* database:   `./bin/basta download prot -d ./taxonomy`
+#### 4.1.2 Set up TaxID mapping database
 
-### 4. Case 2: You plan on using the nt database
+-   Install _prot_ database:   
 
-#### 4.1.1 Download and extract the centrifuge database
 
-```
-mkdir nt_db
-cd nt_db
-wget http://som1.ific.uv.es/nt/nt.cf.7z
-7z e nt.cf.7z
-cd ..
-```
+    ./bin/basta download prot -d ./taxonomy
 
+#### Case 2: You plan on using the nt database
 
-### 4.1.2 Set up TaxID mapping database
+##### 4.1.1 Download and extract the centrifuge database
 
-- Install *gb* database:   `./bin/basta download gb -d ./taxonomy`
+    mkdir nt_db
+    cd nt_db
+    wget http://som1.ific.uv.es/nt/nt.cf.7z
+    7z e nt.cf.7z
+    cd ..
+
+#### 4.1.2 Set up krona mapping database
+
+-   Install _krona_ database:  
+
+
+    ktUpdateTaxonomy.sh ./taxonomy
 
 # Get help
 
-```
-nextflow run maxibor/organdiet --help
-```
+    nextflow run maxibor/organdiet --help
 
 # An example workflow for this pipeline
 
@@ -103,17 +97,19 @@ nextflow run maxibor/organdiet --help
 # Credits
 
 The OrganDiet pipeline uses many tools listed below:
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-- [AdapterRemoval](https://github.com/MikkelSchubert/adapterremoval)
-- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
-- [Samtools](http://www.htslib.org/)
-- [Diamond](https://github.com/bbuchfink/diamond)
-- [Centrifuge](https://ccb.jhu.edu/software/centrifuge/manual.shtml)
-- [BASTA](https://github.com/timkahlke/BASTA)
-- [Krona](https://github.com/marbl/Krona/wiki)
-- [Nextflow](https://www.nextflow.io/)
+
+-   [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+-   [AdapterRemoval](https://github.com/MikkelSchubert/adapterremoval)
+-   [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+-   [Samtools](http://www.htslib.org/)
+-   [Diamond](https://github.com/bbuchfink/diamond)
+-   [Centrifuge](https://ccb.jhu.edu/software/centrifuge/manual.shtml)
+-   [BASTA](https://github.com/timkahlke/BASTA)
+-   [Krona](https://github.com/marbl/Krona/wiki)
+-   [Nextflow](https://www.nextflow.io/)
 
 The author of OrganDiet also got some inspiration and help from the following awesome developers:
-- [Paolo Di Tomasso](https://twitter.com/paoloditommaso)
-- [Phil Ewels](https://twitter.com/tallphil)
-- [Tim Kahlke](https://twitter.com/AdvancedTwigTec)
+
+-   [Paolo Di Tomasso](https://twitter.com/paoloditommaso)
+-   [Phil Ewels](https://twitter.com/tallphil)
+-   [Tim Kahlke](https://twitter.com/AdvancedTwigTec)