3 Trim Poor Reads

3.1 BBDuk trimming poor reads

#!/bin/bash

echo PROGRESS: Read trimming
cd resources/reads

for i in `ls -1 *_1.fastq.gz | sed 's/_1.fastq.gz//'`
  do
  bbduk.sh -Xmx3g \
    in1=$i\_1.fastq.gz \
    in2=$i\_2.fastq.gz \
    out1=trimmed/$i\_1.fastq.gz \
    out2=trimmed/$i\_2.fastq.gz \
    qtrim=r \
    trimq=25 \
    overwrite=True
  done

3.2 FastQC - MultiQC on trimmed reads

#!/bin/bash

echo PROGRESS: FastQC - Getting read quality scores of trimmed reads.

INPUTDIR="resources/reads/trimmed/"
FASTQC="results/qc/fastqc2"
mkdir -p "${FASTQC}"
fastqc "${INPUTDIR}"/*.fastq.gz -o "${FASTQC}"

#!/bin/bash

echo PROGRESS: MultiQC - Getting summary of trimmed read quality scores.

FASTQC="results/qc/fastqc2"
MULTIQC="results/qc/multiqc2"
mkdir -p "${MULTIQC}"
multiqc --force --data-dir "${FASTQC}" -o "${MULTIQC}" --export

3.3 Seqkit on trimmed reads

#!/bin/bash

echo PROGRESS: Getting stats of the trimmed reads.

INPUTDIR="resources/reads/trimmed"
SEQKIT="results/qc/seqkit2"
mkdir -p "${SEQKIT}"
seqkit stat "${INPUTDIR}"/*.fastq.gz >"${SEQKIT}"/seqkit_stats.txt