This workflow was developed in a Linux environment, before running these scripts one should install all dependent packages/software and adopt working environment paths
1.0
- Copy this project to your local directory and access script directory
git clone https://github.com/gvarmaslu/WGS-fosmid-project
cd WGS-fosmid-project/scripts/
- Run script for Cleaning and QC1
bash Run-WGS_1.0_QC.sh > Run-WGS_1.0_QC.sh.log 2>&1
2.0
- Mapped with Ecoli and processed un-mapped reads for assembly
bash Run-WGS_2.0_Align-ecoli-assembly.sh > Run-WGS_2.0_Align-ecoli-assembly.sh.log 2>&1
2.1
- De-novo assembly made with SPAdes "metaplasmid" algorithm
bash Run-WGS_2.1_assembly-plasmid-metaplasmid.sh > Run-WGS_2.1_assembly-plasmid-metaplasmid.sh.log 2>&1
3.0
- Run script for Cleaning and QC2
bash Run-WGS_3.0_QC.sh > Run-WGS_3.0_QC.sh.log 2>&1
3.1
- BLAST for CAZyDB and MEROPS
bash Run-WGS_3.1_BLAST-CAZyDB.sh > Run-WGS_3.1_BLAST-CAZyDB.sh.log 2>&1
4.0
- Script to merge annotations for each sample
### Run-WGS_4.0_Pars-annotation.py INPUT=Inputfile OUTPUT=Outputfile DIR=Directory-fullpath
python Run-WGS_4.0_Pars-annotation.py 9F.txt 9F_anno.tsv /PATH-TO-WORKING-DIR/
4.1
- Script to run annotations for all samples, parse output files and run Clustering analysis with CD-HIT. This script also helps to remove plasmid backbone sequence and to keep insert sequence alone for further downstream analysis
bash Run-WGS_4.1_Pars-annotation_run.sh > Run-WGS_4.1_Pars-annotation_run.sh.log 2>&1
5.0
- Taxonomic classicfication with Kraken2 and visualization with Krona
bash Run-WGS_5.0_kraken2.sh > Run-WGS_5.0_kraken2.sh.log 2>&1
5.1
- PFAM and KEGG analysis
bash Run-WGS_5.1_pfam-KEGG_annotation.sh > Run-WGS_5.1_pfam-KEGG_annotation.sh.log 2>&1