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Ephie Geza, 02/01/2024 06:37 AM

1 1 Ephie Geza 
# Wiki
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## Data location:





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





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``` shell





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/cbio/projects/032/rawdata/fastq





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```





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## Reference data:





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





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``` shell





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/cbio/projects/033/refs/Helicobacter_pylori_MT5135_refseq.fa 





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```





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## Workflow





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### 1. QC:





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Raw reads were quality checked and trimmed using the  kviljoen/fastq_QC pipeline which also trim adpters and filter quality based bbduk





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``` shell





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# For nextflow DSL1 pipeline





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module load nextflow/22.10.7





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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"





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```





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QC reports for raw reads and after trimming can be found in the 





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### 2. AMR profiling





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





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ARGannot