File size: 3,500 Bytes
7102b1b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | #!/bin/bash
set -e
# =============================================================================
# Task 27: Read Downsampling and Assembly Quality Titration
#
# DAG (depth 5, replicated fan-out):
#
# L0: PE reads + reference
# L1: fastp (trim full dataset)
# L2: ├── seqkit sample 25% → megahit → quast
# ├── seqkit sample 50% → megahit → quast
# └── seqkit sample 100% → megahit → quast
# L3: Parse all three QUAST reports
# L4: MERGE (titration report: how coverage affects assembly)
# =============================================================================
THREADS=$(( $(nproc) > 8 ? 8 : $(nproc) ))
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATA="${SCRIPT_DIR}/data"
REF="${SCRIPT_DIR}/reference"
OUT="${SCRIPT_DIR}/outputs"
RES="${SCRIPT_DIR}/results"
REFERENCE="${REF}/reference.fna"
FRACTIONS=("0.25" "0.50" "1.00")
log_step() {
echo "=================================================================="
echo "STEP: $1"
echo "$(date)"
echo "=================================================================="
}
mkdir -p "${OUT}/trimmed" "${RES}"
# L1: Trim
log_step "L1: fastp"
if [ ! -f "${OUT}/trimmed/R1.fastq.gz" ]; then
fastp --in1 "${DATA}/reads_R1.fastq.gz" --in2 "${DATA}/reads_R2.fastq.gz" \
--out1 "${OUT}/trimmed/R1.fastq.gz" --out2 "${OUT}/trimmed/R2.fastq.gz" \
--detect_adapter_for_pe --thread ${THREADS} --json "${OUT}/trimmed/fastp.json"
else echo "Skipping (exists)"; fi
# L2: For each fraction, subsample + assemble + QC
for FRAC in "${FRACTIONS[@]}"; do
FRAC_DIR="${OUT}/frac_${FRAC}"
mkdir -p "${FRAC_DIR}"
log_step "L2: Subsample ${FRAC} + assemble"
if [ ! -f "${FRAC_DIR}/assembly/final.contigs.fa" ]; then
if [ "${FRAC}" = "1.00" ]; then
cp "${OUT}/trimmed/R1.fastq.gz" "${FRAC_DIR}/R1.fastq.gz"
cp "${OUT}/trimmed/R2.fastq.gz" "${FRAC_DIR}/R2.fastq.gz"
else
seqkit sample -p "${FRAC}" -s 42 "${OUT}/trimmed/R1.fastq.gz" -o "${FRAC_DIR}/R1.fastq.gz"
seqkit sample -p "${FRAC}" -s 42 "${OUT}/trimmed/R2.fastq.gz" -o "${FRAC_DIR}/R2.fastq.gz"
fi
megahit -1 "${FRAC_DIR}/R1.fastq.gz" -2 "${FRAC_DIR}/R2.fastq.gz" \
-o "${FRAC_DIR}/assembly" -t ${THREADS} --min-contig-len 500
else echo "Skipping (exists)"; fi
log_step "L2: QUAST ${FRAC}"
if [ ! -f "${FRAC_DIR}/quast/report.tsv" ]; then
quast "${FRAC_DIR}/assembly/final.contigs.fa" -r "${REFERENCE}" \
-o "${FRAC_DIR}/quast" -t ${THREADS}
else echo "Skipping (exists)"; fi
done
# L3-L4: Parse + MERGE
log_step "MERGE"
echo "fraction,total_length,num_contigs,n50,largest_contig,genome_fraction,num_reads" > "${RES}/downsampling_report.csv"
for FRAC in "${FRACTIONS[@]}"; do
FRAC_DIR="${OUT}/frac_${FRAC}"
TOTAL=$(grep "^Total length" "${FRAC_DIR}/quast/report.tsv" | head -1 | cut -f2)
NCTG=$(grep "^# contigs " "${FRAC_DIR}/quast/report.tsv" | head -1 | cut -f2)
N50=$(grep "^N50" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
LARGEST=$(grep "^Largest contig" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
GF=$(grep "^Genome fraction" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
NREADS=$(zcat "${FRAC_DIR}/R1.fastq.gz" | wc -l | awk '{print $1/4}')
echo "${FRAC},${TOTAL},${NCTG},${N50},${LARGEST},${GF},${NREADS}" >> "${RES}/downsampling_report.csv"
done
echo ""
echo "=== Pipeline complete ==="
cat "${RES}/downsampling_report.csv"
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