1. Solanum tuberosum Genome Resources & Structural Annotations

High-quality spliced alignment requires an authoritative reference genome. The doubled monoploid clone Solanum tuberosum Group Phureja clone DM1-3 516 R44 serves as the primary international reference (Spud DB / Ensembl Plants).

2. Raw FASTQ Processing: FastQC and fastp

Polymerase artifacts, sequencing adapters (Illumina TruSeq / Nextera), low-quality bases ($Q < 20$), and polyA/polyG tails (frequent in NovaSeq two-color chemistry) must be scrubbed prior to alignment.

#!/usr/bin/env bash
# Step 1: Automated QC and Adapter/PolyA Trimming for Plant RNA-Seq
mkdir -p qc_raw qc_trimmed trimmed_fastq

# Run FastQC on raw multiplexed FASTQ reads
fastqc -t 8 -o qc_raw/ raw_fastq/*.fastq.gz

# Execute fastp with plant-optimized trimming parameters
for R1 in raw_fastq/*_R1.fastq.gz; do
    R2="${R1/_R1.fastq.gz/_R2.fastq.gz}"
    SAMPLE=$(basename "$R1" _R1.fastq.gz)
    
    echo "Processing Plant Sample: ${SAMPLE}..."
    fastp \
        --in1 "$R1" \
        --in2 "$R2" \
        --out1 "trimmed_fastq/${SAMPLE}_clean_R1.fastq.gz" \
        --out2 "trimmed_fastq/${SAMPLE}_clean_R2.fastq.gz" \
        --detect_adapter_for_pe \
        --trim_poly_g \
        --trim_poly_x \
        --cut_front --cut_tail \
        --cut_mean_quality 20 \
        --length_required 50 \
        --thread 8 \
        --html "qc_trimmed/${SAMPLE}_fastp.html" \
        --json "qc_trimmed/${SAMPLE}_fastp.json"
done

# Aggregate QC metrics across all 18 potato libraries
multiqc qc_trimmed/ -o multiqc_report/