QC and Pre-processing

3. QC and Pre-processing#

3.1. Steps#

  1. Inspect quality with FastQC / MultiQC.

  2. Trim adapters and low-quality bases using fastp or cutadapt.

  3. Optionally remove host reads by mapping to the host genome.

3.2. Example (fastp)#

fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \
      -o clean_R1.fastq.gz -O clean_R2.fastq.gz \
      --detect_adapter_for_pe --thread 8 --html fastp_report.html
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