Agent skill

bio-workflows-genome-assembly-pipeline

End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.

View SKILL.md on GitHub Repository
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Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/data/genome-assembly-pipeline

SKILL.md

Genome Assembly Pipeline

Complete workflow from sequencing reads to polished, quality-assessed genome assembly.

Workflow Overview

Reads (short and/or long)
    |
    v
[1. QC & Filtering] -----> fastp, NanoPlot
    |
    v
[2. Assembly] -----------> SPAdes (short) or Flye (long)
    |
    v
[3. Polishing] ----------> Pilon (short) or medaka (long)
    |
    v
[4. QC Assessment] ------> QUAST, BUSCO
    |
    v
Final polished assembly

Path A: Short-Read Assembly (SPAdes)

Step 1: QC

bash
fastp -i reads_R1.fastq.gz -I reads_R2.fastq.gz \
    -o trimmed_R1.fq.gz -O trimmed_R2.fq.gz \
    --detect_adapter_for_pe \
    --qualified_quality_phred 20 \
    --length_required 50 \
    --html qc_report.html

Step 2: Assembly with SPAdes

bash
# Standard bacterial assembly
spades.py \
    -1 trimmed_R1.fq.gz \
    -2 trimmed_R2.fq.gz \
    -o spades_output \
    --careful \
    -t 16 \
    -m 64

# For isolate genomes
spades.py --isolate \
    -1 trimmed_R1.fq.gz \
    -2 trimmed_R2.fq.gz \
    -o spades_output \
    -t 16

Step 3: Polishing with Pilon

bash
# Align reads to assembly
bwa index spades_output/scaffolds.fasta
bwa mem -t 16 spades_output/scaffolds.fasta \
    trimmed_R1.fq.gz trimmed_R2.fq.gz | \
    samtools sort -@ 4 -o aligned.bam
samtools index aligned.bam

# Polish
pilon --genome spades_output/scaffolds.fasta \
    --frags aligned.bam \
    --output polished \
    --threads 16

Path B: Long-Read Assembly (Flye)

Step 1: QC

bash
# NanoPlot for long-read QC
NanoPlot --fastq reads.fastq.gz \
    --outdir nanoplot_output \
    --threads 8

Step 2: Assembly with Flye

bash
# ONT raw reads
flye --nano-raw reads.fastq.gz \
    --out-dir flye_output \
    --threads 16 \
    --genome-size 5m

# ONT HQ reads (sup/dna_r10)
flye --nano-hq reads.fastq.gz \
    --out-dir flye_output \
    --threads 16 \
    --genome-size 5m

# PacBio HiFi
flye --pacbio-hifi reads.fastq.gz \
    --out-dir flye_output \
    --threads 16 \
    --genome-size 5m

Step 3: Polishing with medaka

bash
# Polish with medaka (for ONT)
medaka_consensus \
    -i reads.fastq.gz \
    -d flye_output/assembly.fasta \
    -o medaka_output \
    -t 16 \
    -m r1041_e82_400bps_sup_v4.3.0  # Match your basecalling model

Path C: Hybrid Assembly

bash
# Flye with long reads, then polish with short reads
flye --nano-hq long_reads.fastq.gz \
    --out-dir flye_output \
    --threads 16 \
    --genome-size 5m

# Polish with short reads using Pilon
bwa index flye_output/assembly.fasta
bwa mem -t 16 flye_output/assembly.fasta \
    short_R1.fq.gz short_R2.fq.gz | \
    samtools sort -@ 4 -o aligned.bam
samtools index aligned.bam

pilon --genome flye_output/assembly.fasta \
    --frags aligned.bam \
    --output hybrid_polished \
    --threads 16

Step 4: Quality Assessment

QUAST

bash
quast.py polished.fasta \
    -r reference.fasta \
    -g genes.gff \
    -o quast_output \
    -t 8

# Without reference
quast.py polished.fasta \
    -o quast_output \
    -t 8

BUSCO

bash
# Download lineage database
busco --download bacteria_odb10

# Run BUSCO
busco -i polished.fasta \
    -l bacteria_odb10 \
    -o busco_output \
    -m genome \
    -c 8

Parameter Recommendations

Tool Parameter Bacteria Eukaryote
SPAdes --careful Yes Optional
SPAdes -m 64GB 256GB+
Flye --genome-size 5m Species-specific
Flye --meta If metagenome No
BUSCO -l bacteria_odb10 eukaryota_odb10

Troubleshooting

Issue Likely Cause Solution
Fragmented assembly Low coverage, repetitive genome Increase coverage, use long reads
Low N50 Short reads only Add long reads for scaffolding
Low BUSCO Incomplete assembly, wrong lineage Check coverage, try different lineage
Assembly too large Contamination, heterozygosity Filter reads, check for contamination

Complete Pipeline Script

bash
#!/bin/bash
set -e

THREADS=16
GENOME_SIZE="5m"
LONG_READS="long_reads.fastq.gz"
SHORT_R1="short_R1.fastq.gz"
SHORT_R2="short_R2.fastq.gz"
BUSCO_LINEAGE="bacteria_odb10"
OUTDIR="assembly_results"

mkdir -p ${OUTDIR}/{qc,assembly,polished,quast,busco}

# Step 1: QC
echo "=== QC ==="
NanoPlot --fastq ${LONG_READS} --outdir ${OUTDIR}/qc/nanoplot -t ${THREADS}
fastp -i ${SHORT_R1} -I ${SHORT_R2} \
    -o ${OUTDIR}/qc/short_R1.fq.gz -O ${OUTDIR}/qc/short_R2.fq.gz \
    --html ${OUTDIR}/qc/fastp.html

# Step 2: Assembly with Flye
echo "=== Assembly ==="
flye --nano-hq ${LONG_READS} \
    --out-dir ${OUTDIR}/assembly \
    --threads ${THREADS} \
    --genome-size ${GENOME_SIZE}

# Step 3: Polish with short reads
echo "=== Polishing ==="
bwa index ${OUTDIR}/assembly/assembly.fasta
bwa mem -t ${THREADS} ${OUTDIR}/assembly/assembly.fasta \
    ${OUTDIR}/qc/short_R1.fq.gz ${OUTDIR}/qc/short_R2.fq.gz | \
    samtools sort -@ 4 -o ${OUTDIR}/polished/aligned.bam
samtools index ${OUTDIR}/polished/aligned.bam

pilon --genome ${OUTDIR}/assembly/assembly.fasta \
    --frags ${OUTDIR}/polished/aligned.bam \
    --output ${OUTDIR}/polished/final \
    --threads ${THREADS}

# Step 4: QC
echo "=== Quality Assessment ==="
quast.py ${OUTDIR}/polished/final.fasta -o ${OUTDIR}/quast -t ${THREADS}
busco -i ${OUTDIR}/polished/final.fasta -l ${BUSCO_LINEAGE} \
    -o busco -m genome -c ${THREADS} --out_path ${OUTDIR}

echo "=== Assembly Complete ==="
echo "Final assembly: ${OUTDIR}/polished/final.fasta"
cat ${OUTDIR}/quast/report.txt

Related Skills

  • genome-assembly/short-read-assembly - SPAdes details
  • genome-assembly/long-read-assembly - Flye, Canu, Hifiasm
  • genome-assembly/assembly-polishing - Pilon, medaka, Racon
  • genome-assembly/assembly-qc - QUAST, BUSCO metrics

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