kibet-gilbert/WGS_Assembly

Reference based and de novo assembly of whole genomes ## **Introduction** This is a follow up on the series of bioinformatics training sessions for the EAST African Network for Bioinformatics Training (EANBiT) held at KEMRI wellcome Trust, Kilifi Campus. This session focuses on the main procedure of WGS (whole genome sequencing) reference based and de novo assembly. NOTE: It may be necessary to make slight changes along the way. ## **Getting started** We need to load the programs we intend to use way before hand. Once that is done, create a directory named "WGS" in your home directory and navigate to it. This is where the analysis will be carried out. As we go on, we shall be creating sub-directories accordingly to ensure that intermediate outputs can be refered to easily whenever needed for downstream analyses. ```{r,eval=FALSE,error=FALSE,warning=FALSE,message=FALSE,echo=TRUE} mkdir WGS ``` Inside WGS, make a directory `data` to store data. Download the data from a repository using `wget` program. ```{r,eval=FALSE,error=FALSE,warning=FALSE,message=FALSE,echo=TRUE} mkdir "$HOME/WGS/data" cd data wget raw.githubusercontent.com wget raw.githubusercontent.com ``` To confirm that the links have been successfully created, list the contents of the folder using the `ls` command. If the data is compressed (i.e .gz files), uncompress them using `gunzip *` ## **Quality control check** Here we use `fastqc`, it is necessary that we store quality control files for easy reference. In WGS, create a sub-directory qcresults, this is where the fastqc results will be stored. After that, do the quality checks; ```{r,eval=FALSE,error=FALSE,warning=FALSE,message=FALSE,echo=TRUE} mkdir "$HOME/WGS/qcresults" fastqc "$HOME/WGS/data/*" -o "$HOME/WGS/qcresults" ``` Once this is done, navigate to `qcresults` and download the ".html" files to local machine and open them in any browser. This report can be used to assess quality distribution, le …