Karumata

HIV pipeline

How to run

Assume that the fastq files are in the dataSet_Illumina_HIV directory and you intend to put the results in the directory named result.

nextflow run Karumata \
--illumina \
--reads dataSet_Illumina_HIV \
--out_dir result 

Note

Replace --illumina with --ont if you are dealing with ONT reads.

To verify results

Stanford University HIV Drug Resistance Database will be used after creating codfreq files from the raw fastq files.

Warning

An error may be encountered in codfreq's fastp v0.23.4.
ERROR: sequence and quality have different length

1. Install Docker Engine.

2. Install the modified version of codfreq (i.e., a docker image with the older fastp v0.20.1).

   sudo curl -sL https://raw.githubusercontent.com/omic-analytics/Karumata/main/assets/modified_fastq2codfreq -o /usr/local/bin/fastq2codfreq
   
   sudo chmod +x /usr/local/bin/fastq2codfreq
   

3. Download the HIV-1 alignment profile.

   wget https://raw.githubusercontent.com/omic-analytics/Karumata/main/assets/HIV1.json
   

4. Create codfreq files from raw fastq files using codfreq.

   fastq2codfreq -r ./path/to/HIV1.json -d ./fastq_4codefreq/
   

5. Upload the codfreq files to Stanford HIVdb.