diff --git a/README.md b/README.md index c692649..802f470 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ - ## 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:G3nom3s4u@ussd-ftp.illumina.com/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:G3nom3s4u@ussd-ftp.illumina.com/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)