Wiki¶

Data location:¶

The data in FASTQ format was sent via WeTransfer, downloaded and uploaded to ilifu

/cbio/projects/032/rawdata/fastq

Reference data:¶

Currently in project 033 on ilifu: Helicobacter pylori strain: MT5135 (RefSeq accession no. CP071982.1) (n=2)

/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

# 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¶

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 for previous projects as:

ARGannot