03. Illumina Adapter removal

Remove Illumina Adapters.

Input Files

ls Sample_reads

10_S10_L001_R1_001.fastq.gz

10_S10_L001_R2_001.fastq.gz

11_S11_L001_R1_001.fastq.gz

11_S11_L001_R2_001.fastq.gz

Command

bash Scripts/2-fastqc_reports.sh

Ouputs

The above script will create Illumina_Adapter_Removed folder.

• Illumina_Adapter_Removed -The output folder
• .fastq.gz - Adapter removed fastq files
• Illumina_Adapter_Removed/stats - Summary of adapter mathced for each sample