Quality control

Graph

Usage

Single sample: [preprocessing.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/preprocessing.sh)

bash preprocessing.sh -s [SAMPLE_NAME]

Multiple samples: [wrapper_preprocessing.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_preprocessing.sh )

bash wrapper_preprocessing.sh

Note: To run [wrapper_preprocessing.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_preprocessing.sh) you must have generated the sample name list with Sample Name list generator

In a nutshell...

• 1. Creates necessary directories.
• 2. Runs quality control of the raw reads with fastQC.
• 3. Performs quality trimming with Trimmommatic.
• 4. Runs quality control of the trimmed reads with fastQC
• 5. Prepares directory structure to create unified quality report

I/O

• Parameters:

  • -s sampleName = Name of the sample
  • -h = shows help

• Input Directory:

  • rawDir= Directory where the raw reads are located (ANALYSIS/00-reads/)

    • Input files: (In rawDir)
      • sampleName_*_R1_*.fastq.gz
      • sampleName_*_R2_*.fastq.gz

• Output Directories:

  • samplePreProQCDir = Raw reads quality analysis directory. (ANALYSIS/01-fastqc/sampleName)

    • Output files: (In samplePreProQCDir)
      • sampleName_*_R1_*.fastqc.html: HTML file with the quality report for R1 raw reads.
      • sampleName_*_R2_*.fastqc.html: HTML file with the quality report for R2 raw reads.
      • sampleName_*_R1_*.fastqc.zip: compressed file with the quality report files for R1 raw reads generated by fastQC.
      • sampleName_*_R2_*.fastqc.zip: compressed file with the quality report files for R2 raw reads generated by fastQC.
      • sampleName_preQC.log: log file for the quality analysis.

  • samplePostProDir = Trimmed reads directory. (ANALYSIS/02-preprocessing/sampleName)

    • Output files: (In samplePostProDir)
    • sampleName_R1_paired.fastq: fastq file with R1 trimmed paired reads.
    • sampleName_R2_paired.fastq: fastq file with R2 trimmed paired reads.
    • sampleName_R1_unpaired.fastq: fastq file with R1 trimmed unpaired reads.
    • sampleName_R2_unpaired.fastq: fastq file with R2 trimmed unpaired reads.
    • sampleName_postQC.log: log of the trimming process.

Note: Only the paired reads are used in the rest of the analysis

• samplePostProQCDir = Trimmed reads quality analysis directory. (ANALYSIS/03-preproQC/sampleName)

  • Output files: (In samplePostProQCDir)
  • sampleName_R1_paired.fastqc.html: HTML file with the quality report for R1 trimmed reads.
  • sampleName_R2_paired.fastqc.html: HTML file with the quality report for R2 trimmed reads.
  • sampleName_R1_paired.fastqc.zip: compressed file with the quality report files for R1 trimmed reads generated by fastQC.
  • sampleName_R2_paired.fastqc.zip: compressed file with the quality report files for R2 trimmed reads generated by fastQC.
  • sampleName_postQC.log: log file for the quality analysis.

• sampleStatsDir = Quality report html directory. (ANALYSIS/99-stats/sampleName)