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¶

We used three DBs for AMR ARGannot_r3, CARD_v3.0.8 and ResFinder:

ARGannot