Investigating the prevalence of Helicobacter Pylori in South Africa

# Wiki

## Data location:
The data in FASTQ format was sent via WeTransfer, downloaded and uploaded to ilifu
``` shell
/cbio/projects/032/rawdata/fastq
```

## Reference data:
Currently in project 033 on ilifu: Helicobacter pylori strain: MT5135 (RefSeq accession no. CP071982.1) (n=2)
``` shell
/cbio/projects/033/refs/Helicobacter_pylori_MT5135_refseq.fa
```

## Workflow

### 1. QC:
Raw reads were quality checked and trimmed using the kviljoen/fastq_QC pipeline which also trim adpters and filter quality based bbduk
``` shell
# For nextflow DSL1 pipeline
module load nextflow/22.10.7

nextflow run kviljoen/fastq_QC --reads '/cbio/projects/032/rawdata/fastq/*_R{1,2}_001.fastq.gz' -profile ilifu -resume --email "ephie.geza@uct.ac.za"
```
QC reports for raw reads and after trimming can be found in the
### 2. AMR profiling
We The preference from Clinton is to do AMR profiling with the ResFinder DB. I'm getting errors there that I think relate to the header formatting though so in the interim have run with the ARG_annot DB that we used three DBs for AMR ARGannot_r3, CARD_v3.0.8 and ResFinder: previous projects as:

ARGannot