bio-genome-assembly-long-read-assembly — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited bio-genome-assembly-long-read-assembly (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
Reference examples tested with: Canu 2.2+, Flye 2.9+, hifiasm 0.19+, wtdbg2 2.5+
Before using code patterns, verify installed versions match. If versions differ:
<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Assemble a genome from long reads" → Build a contiguous de novo assembly from ONT or PacBio reads, producing complete or near-complete chromosomes.
flye --nano-raw reads.fq -o output (ONT), canu -p asm -d output -nanopore reads.fq (ONT/PacBio)| Tool | Speed | Memory | Best For |
|---|---|---|---|
| Flye | Fast | Moderate | General purpose, bacteria, ONT |
| Canu | Slow | High | High accuracy, complex genomes |
| Wtdbg2 | Very fast | Low | Draft assemblies |
Note: For PacBio HiFi data, see the dedicated hifi-assembly skill which covers hifiasm.
conda install -c bioconda flye# Oxford Nanopore
flye --nano-raw reads.fastq.gz --out-dir flye_output --threads 16
# PacBio CLR
flye --pacbio-raw reads.fastq.gz --out-dir flye_output --threads 16
# PacBio HiFi
flye --pacbio-hifi reads.fastq.gz --out-dir flye_output --threads 16| Option | Read Type |
|---|---|
--nano-raw | ONT regular reads |
--nano-corr | ONT corrected reads |
--nano-hq | ONT Q20+ reads (Guppy 5+) |
--pacbio-raw | PacBio CLR |
--pacbio-corr | PacBio corrected |
--pacbio-hifi | PacBio HiFi/CCS |
| Option | Description |
|---|---|
--out-dir | Output directory |
--threads | Number of threads |
--genome-size | Estimated genome size (e.g., 5m, 100m) |
--iterations | Polishing iterations (default: 1) |
--meta | Metagenome mode |
--plasmids | Recover plasmids |
--keep-haplotypes | Don't collapse haplotypes |
--scaffold | Enable scaffolding |
# Estimate if unknown
flye --nano-raw reads.fq.gz --out-dir output --genome-size 5m
# Size formats: 1000, 1k, 1m, 1gflye_output/
├── assembly.fasta # Final assembly
├── assembly_graph.gfa # Assembly graph
├── assembly_info.txt # Contig statistics
└── flye.log # Log fileflye \
--nano-raw bacteria.fastq.gz \
--out-dir bacteria_assembly \
--genome-size 5m \
--threads 16flye \
--nano-raw metagenome.fastq.gz \
--out-dir meta_assembly \
--meta \
--threads 32flye \
--nano-raw isolate.fastq.gz \
--out-dir assembly \
--plasmids \
--threads 16conda install -c bioconda canu# ONT reads
canu -p assembly -d canu_output genomeSize=5m -nanopore reads.fastq.gz
# PacBio HiFi
canu -p assembly -d canu_output genomeSize=5m -pacbio-hifi reads.fastq.gz| Option | Description |
|---|---|
-p | Assembly prefix |
-d | Output directory |
genomeSize= | Estimated size (required) |
maxThreads= | Max threads |
maxMemory= | Max memory (e.g., 64g) |
useGrid=false | Disable grid execution |
correctedErrorRate= | Expected error rate |
| Option | Read Type |
|---|---|
-nanopore | ONT reads |
-nanopore-raw | ONT raw (deprecated) |
-pacbio | PacBio CLR |
-pacbio-hifi | PacBio HiFi/CCS |
canu -p asm -d output genomeSize=5m \
-nanopore reads.fq.gz \
useGrid=false \
maxThreads=16 \
maxMemory=32gcanu -p asm -d output genomeSize=5m \
-pacbio-hifi reads.fq.gz \
correctedErrorRate=0.01canu_output/
├── assembly.contigs.fasta # Contigs
├── assembly.unassembled.fasta
├── assembly.report
└── assembly.seqStore/conda install -c bioconda wtdbg# Assemble
wtdbg2 -x ont -g 5m -t 16 -i reads.fq.gz -o draft
# Consensus
wtpoa-cns -t 16 -i draft.ctg.lay.gz -o draft.ctg.fa| Preset | Platform |
|---|---|
-x ont | ONT R9 |
-x ccs | PacBio HiFi |
-x rs | PacBio CLR |
-x sq | ONT R10 |
Goal: Run end-to-end long-read assembly pipelines from raw reads to contigs.
Approach: Use Flye for initial assembly, optionally followed by short-read polishing.
#!/bin/bash
set -euo pipefail
READS=$1
OUTDIR=$2
SIZE=${3:-5m}
echo "=== ONT Bacterial Assembly ==="
# Flye assembly
flye \
--nano-raw $READS \
--out-dir ${OUTDIR}/flye \
--genome-size $SIZE \
--threads 16
# Stats
echo "Assembly statistics:"
cat ${OUTDIR}/flye/assembly_info.txt
echo "Assembly: ${OUTDIR}/flye/assembly.fasta"#!/bin/bash
set -euo pipefail
LONG=$1
SHORT_R1=$2
SHORT_R2=$3
OUTDIR=$4
# 1. Long-read assembly with Flye
flye --nano-raw $LONG --out-dir ${OUTDIR}/flye --genome-size 5m --threads 16
# 2. Polish with short reads (Pilon)
# See assembly-polishing skill| Metric | Bacterial | Eukaryotic |
|---|---|---|
| Contigs | 1-10 | 100-1000+ |
| N50 | >1 Mb | Variable |
| Complete chromosomes | Often | Rare |
~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.