First, SINGLE-END `fastq` files must be quality-filtered.
We provide a complete workflow to perform preprocessing of sequencing ngs raw data. This workflow is available as a github repositories here : [clean-fastq](https://github.com/Grelot/clean-fastq)
We provide a complete workflow to perform preprocessing of sequencing ngs raw data. This workflow is available as a github repository here : [clean-fastq](https://github.com/Grelot/clean-fastq)
## Set up
### Wildcards
*`{species}` : any complete project (in our case we have 2 projects : mullus and diplodus)
*`{species}` : any complete project (in our case we have 2 projects : _mullus_ and _diplodus_)
*`{lane}` : any physical lane on a flow cell that goes into the sequencing machine. We have many `{lane}` by `{species}`
*`{barcode}` : any DNA sequence attached to a reads which belong to a sample. We have many `{barcode}` by `{lane}` by `{species}`
