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Bio Genome Assembly Long Read Assembly · FreedomIntelligence | DecimalAI

Bio Genome Assembly Long Read Assembly

NewSkillScoreMaintained

bio-genome-assembly-long-read-assembly

De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.

scienceby FreedomIntelligence

Links this skill to your agents and keeps it current with the author’s updates.

Automatic

Research pack

1 · One-time — install the CLI (docs ↗)

pip install decimalai

2 · Get the skill — writes .claude/skills/bio-genome-assembly-long-read-assembly/SKILL.md

decimalai skills pull bio-genome-assembly-long-read-assembly --out .claude/skills/

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/bio-genome-assembly-long-read-assembly/SKILL.md https://app.decimal.ai/s/bio-genome-assembly-long-read-assembly/SKILL.md

Raw file: /s/bio-genome-assembly-long-read-assembly/SKILL.md ↗ · machine-readable summary at /s/bio-genome-assembly-long-read-assembly.json ↗

In productionGlobal

how this skill behaves on real traffic · last 30 days

No production data for this skill yet — usage numbers appear here once agents start running it.

Anonymized aggregate across every org using this skill — proof from real production use, not a demo.

Does this skill help? · Benchmark: with vs. withoutsign in to run this on your agents

22 test cases from the publisher’s eval.yaml · each run twice on gemini-3.6-flash — with the skill injected, then without · last run 49d ago

—+204% tokens0% turns95% of whole cases pass with skill (21/22)

Test case	Without → With	Effect	Δ tokens	Δ turns
case-11	✗→✓	▲ Improved	448%	0%
case-15	✗→✓	▲ Improved	39%	0%
case-08	✓→✗	▼ Worse	271%	0%
case-09	✓→✓	＝ Same ✓	266%	0%
case-10	✓→✓	＝ Same ✓	185%	0%

Showing 5 of 22 cases

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/1/2026

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

FreedomIntelligence / OpenClaw-Medical-Skills

skills/bio-genome-assembly-long-read-assembly/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v2

Skill contents

SKILL.md

<!--

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

All Rights Reserved.

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

Provenance: Authenticated by MD BABU MIA

-->

Long-Read Assembly

Assemble genomes from Oxford Nanopore (ONT) or PacBio long reads for highly contiguous assemblies.

Tool Comparison

| 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.

Flye

Installation

bash
conda install -c bioconda flye

Basic Usage

bash
# 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

Read Type Options

| 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 |

Key Options

| 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 |

Genome Size Estimation

bash
# Estimate if unknown
flye --nano-raw reads.fq.gz --out-dir output --genome-size 5m

# Size formats: 1000, 1k, 1m, 1g

Output Files

flye_output/
├── assembly.fasta       # Final assembly
├── assembly_graph.gfa   # Assembly graph
├── assembly_info.txt    # Contig statistics
└── flye.log             # Log file

Bacterial Assembly

bash
flye \
    --nano-raw bacteria.fastq.gz \
    --out-dir bacteria_assembly \
    --genome-size 5m \
    --threads 16

Metagenome Assembly

bash
flye \
    --nano-raw metagenome.fastq.gz \
    --out-dir meta_assembly \
    --meta \
    --threads 32

With Plasmid Recovery

bash
flye \
    --nano-raw isolate.fastq.gz \
    --out-dir assembly \
    --plasmids \
    --threads 16

Canu

Installation

bash
conda install -c bioconda canu

Basic Usage

bash
# 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

Key Options

| 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 |

Read Type Options

| Option | Read Type | |--------|-----------| | -nanopore | ONT reads | | -nanopore-raw | ONT raw (deprecated) | | -pacbio | PacBio CLR | | -pacbio-hifi | PacBio HiFi/CCS |

Fast Mode

bash
canu -p asm -d output genomeSize=5m \
    -nanopore reads.fq.gz \
    useGrid=false \
    maxThreads=16 \
    maxMemory=32g

High-Quality Mode (PacBio HiFi)

bash
canu -p asm -d output genomeSize=5m \
    -pacbio-hifi reads.fq.gz \
    correctedErrorRate=0.01

Output Files

canu_output/
├── assembly.contigs.fasta   # Contigs
├── assembly.unassembled.fasta
├── assembly.report
└── assembly.seqStore/

Wtdbg2 (Fast Draft)

Installation

bash
conda install -c bioconda wtdbg

Basic Usage

bash
# 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

Platform Presets

| Preset | Platform | |--------|----------| | -x ont | ONT R9 | | -x ccs | PacBio HiFi | | -x rs | PacBio CLR | | -x sq | ONT R10 |

Complete Workflows

ONT Bacterial Assembly

bash
#!/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"

Hybrid Assembly (Long + Short)

bash
#!/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

Quality Expectations

| Metric | Bacterial | Eukaryotic | |--------|-----------|------------| | Contigs | 1-10 | 100-1000+ | | N50 | >1 Mb | Variable | | Complete chromosomes | Often | Rare |

Troubleshooting

Low Contiguity

Check coverage (need >30x)
Try increasing iterations in Flye
Consider supplementing with short reads

Memory Issues

Use Flye (more memory efficient)
Reduce threads
Filter reads by length/quality

Misassemblies

Polish with Pilon/medaka
Validate with short reads
Check for contamination

Related Skills

hifi-assembly - PacBio HiFi assembly with hifiasm
assembly-polishing - Polish long-read assemblies
assembly-qc - QUAST and BUSCO assessment
short-read-assembly - Hybrid with Illumina
long-read-sequencing - Read QC and alignment

Illustrative Want to see what bio-genome-assembly-long-read-assembly would put in front of your model? Preview the rendered body and check its trigger phrases — no LLM call, no signup.

Latest benchmark · publisher runVerified

8/2/2026, 16:13 UTC · 22 cases

Measured on 21 comparable cases — below the 22 needed to publish a lift, so this result is shown here but not on the registry card or leaderboard.

Lift

50% vs 50%

Agent turns

1.0 vs 1.0

Tokens

+204%

2,457.9 vs 809

fail → pass · 2pass → pass · 19pass → fail · 1

Per-case results (22)

Case	Status	Duration (ms)			Turns			Tokens			Tool calls
Case	Status	Without	With	Δ	Without	With	Δ	Without	With	Δ	Without	With	Δ
case-09 Write a Canu command to assemble ONT reads `reads.fq.gz` (`-p test`, `-d test_out`, genome size 10m) on a standalone workstation without submitting jobs to SGE/SLURM clusters.	pass→pass	3,373	3,301	-2%	1	1	0%	700	2,562	+266%	0	0	—
case-10 Construct a Canu command for ONT reads `reads.fq.gz` with project `sample` in directory `out_dir` (genome size 300m) restricting execution to 16 threads and 64 gigabytes of memory on a single machine without grid execution.	pass→pass	3,931	2,988	-24%	1	1	0%	888	2,533	+185%	0	0	—
case-19 Write the Flye invocation to assemble PacBio HiFi reads stored in `hifi_input.fastq.gz` into `hifi_flye_out` using 16 threads.	pass→pass	2,424	1,827	-25%	1	1	0%	484	2,224	+360%	0	0	—
case-20 Generate a command using `hifiasm` to produce a phased diploid assembly from PacBio HiFi reads `hifi.fq.gz` using 32 threads with output prefix `phased_asm`.	pass→pass	3,690	3,694	+0%	1	1	0%	706	2,671	+278%	0	0	—
case-05 How do you run Flye on Nanopore reads `haplo.fq.gz` into `out_hap` with 16 threads if you want to prevent alternative haplotypes from being collapsed into a single pseudo-haplotype?	pass→pass	4,532	2,816	-38%	1	1	0%	871	2,472	+184%	0	0	—
case-06 Write a Flye command to assemble legacy PacBio Continuous Long Reads (CLR) in `clr_reads.fastq.gz` into `clr_out` using 12 threads.	pass→pass	3,349	1,207	-64%	1	1	0%	657	2,143	+226%	0	0	—
case-07 Provide the command line for Flye operating on ONT raw reads `reads.fq.gz` to output to `dir_out` using 16 threads while running 3 polishing iterations instead of the default single round.	pass→pass	2,984	2,161	-28%	1	1	0%	613	2,300	+275%	0	0	—
case-08 Specify a Canu assembly command for Oxford Nanopore reads `ont.fastq.gz` with project name `ecoli`, output directory `canu_ecoli`, and an estimated genome size of 5.0 Mb.	pass→fail	3,479	2,988	-14%	1	1	0%	675	2,506	+271%	0	0	—
case-01 Write a bash command to run Flye on high-accuracy Q20+ Oxford Nanopore reads stored in `ont_q20.fq.gz`. Output to `out_dir` using 16 threads. Do not use generic raw read flags.	pass→pass	3,945	2,249	-43%	1	1	0%	660	2,383	+261%	0	0	—
case-02 Provide the Flye command to assemble a complex environmental sample from Oxford Nanopore reads in `meta.fastq.gz` into `meta_out` using 32 threads, accounting for uneven organism coverage.	pass→pass	4,052	2,813	-31%	1	1	0%	733	2,456	+235%	0	0	—
case-03 Construct a Flye invocation for a bacterial isolate read set `isolate.fastq.gz` outputting to `bact_out` with 16 threads, ensuring extra circular extrachromosomal elements are explicitly recovered.	pass→pass	6,518	4,603	-29%	1	1	0%	1,291	2,740	+112%	0	0	—
case-04 Write a Flye execution command for standard Nanopore reads in `reads.fq.gz` targeting an estimated genome size of 5 megabases into directory `asm_out` using 8 threads.	pass→pass	4,518	1,872	-59%	1	1	0%	876	2,292	+162%	0	0	—
case-11 Provide the Canu command to assemble PacBio HiFi reads `hifi.fastq.gz` with project prefix `hifi_asm`, output directory `hifi_out`, genome size 20m, explicitly configuring the corrected error rate threshold to 1%.	fail→pass	6,492	2,997	-54%	1	1	0%	475	2,605	+448%	0	0	—
case-12 Write the first stage command using `wtdbg2` to assemble Oxford Nanopore R9 reads in `ont_reads.fq.gz` for a 5Mb genome using 16 threads, saving prefix output as `draft_out`.	pass→pass	4,875	2,248	-54%	1	1	0%	914	2,383	+161%	0	0	—
case-13 Construct the initial `wtdbg2` assembly step for PacBio HiFi reads `hifi_reads.fq.gz` targeting a 100Mb genome using 24 threads, writing output to prefix `hifi_draft`.	pass→pass	5,741	2,713	-53%	1	1	0%	1,146	2,521	+120%	0	0	—
case-14 After running `wtdbg2 -i reads.fq.gz -o draft`, what companion binary and arguments produce the polished FASTA contigs `draft.ctg.fa` from `draft.ctg.lay.gz` using 16 threads?	pass→pass	2,947	2,585	-12%	1	1	0%	589	2,472	+320%	0	0	—
case-15 Recommend and write a 2-step command pipeline (assembly followed by layout consensus) for producing an initial draft genome assembly as fast as possible with minimal memory usage from ONT reads `fast_reads.fq.gz` for a 5Mb organism into prefix `fast_draft` using 16 threads.	fail→pass	10,316	4,348	-58%	1	1	0%	2,099	2,924	+39%	0	0	—
case-16 If Flye is run with `--out-dir output_run`, what exact filename within `output_run` contains the final sequence contigs in FASTA format?	pass→pass	2,226	1,407	-37%	1	1	0%	372	2,157	+480%	0	0	—
case-17 What is the relative file path containing the assembled contigs produced by Canu when executed with `-p my_spec` and `-d result_dir`?	pass→pass	2,911	2,086	-28%	1	1	0%	530	2,321	+338%	0	0	—
case-18 Write a Flye command for Nanopore reads `reads.fq.gz` (`--out-dir scaffold_out`, 16 threads) explicitly enabling the internal scaffolding step across repeat regions.	pass→pass	4,538	2,357	-48%	1	1	0%	858	2,338	+172%	0	0	—
case-21 Write a command to evaluate the lineage completeness of a newly assembled genome `assembly.fasta` against the `bacteria_odb10` lineage dataset using BUSCO with 8 threads.	pass→pass	3,323	2,937	-12%	1	1	0%	621	2,452	+295%	0	0	—
case-22 Provide a bash command using Medaka to polish an existing draft genome `draft.fasta` with Oxford Nanopore reads `reads.fastq.gz` using the `r941_min_high_g360` model.	pass→pass	3,500	3,974	+14%	1	1	0%	706	2,766	+292%	0	0	—

These cases were also screened by the skill’s intent / safety pass.See the Trust review ↗Reproduce this benchmark in Colab ↗

How this skill was measured

DecimalAI ran this skill against gemini-3.6-flash twice over the same eval suite — once with the skill loaded and once without — and compared the two runs case by case. 22 cases were attempted, and 21 counted toward the lift figure. The other 1 produced results that are not comparable between the two arms, so they are excluded from the headline rather than averaged into it. The headline lift of 0 percentage points is the difference between those two pass rates over the 21 comparable cases. 1 case got worse with the skill loaded, and it is included in that figure.

Model measured: gemini-3.6-flash
Graded by: gemini-3.6-flash
Grading method: judged
Verification: verified
Pass rate without the skill: 50%
Pass rate with the skill: 50%
Cases attempted: 22
Cases counted toward lift: 21
Cases that regressed: 1
Skill version measured: v2
Run completed: 8/2/2026, 16:13 UTC

Measured example — same prompt, with vs. without the skill · from the benchmark run · case case-15

Prompt

Recommend and write a 2-step command pipeline (assembly followed by layout consensus) for producing an initial draft genome assembly as fast as possible with minimal memory usage from ONT reads `fast_reads.fq.gz` for a 5Mb organism into prefix `fast_draft` using 16 threads.

Without the skill loaded, the model failed this case. With it loaded, the same prompt on the same model passed. This is one improved case from the latest verified run; every case, including any that regressed, is in the table above.

Show both answers

SkillScore blends 4 signalsno signals yet

BenchmarkRun a verified benchmark with positive lift

Live evalNeeds ≥10 evaluated traces in 30 days

AI ratingNeeds ≥10 rated traces

AdoptionNeeds ≥10 serves across ≥2 orgs in 30 days

Efficiency · separate axis (at equal correctness)+0% turns+225% tokens

Shown for transparency; not credited unless a verified run shows no correctness regression.

No signals yet — run a benchmark or collect evaluated traces to earn a score.

Verified on gemini-3.6-flash · re-tested 49 days ago

Model	Method	Date	Lift
gemini-3.6-flash	verified	7/26/2026	+14%

Other measured skills in the registry, with their headline benchmark lift.

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Bio Genome Assembly Long Read Assembly

SkillSafety

Source

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

All Rights Reserved.

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

Provenance: Authenticated by MD BABU MIA

Long-Read Assembly

Tool Comparison

Flye

Installation

Basic Usage

Read Type Options

Key Options

Genome Size Estimation

Output Files

Bacterial Assembly

Metagenome Assembly

With Plasmid Recovery

Canu

Installation

Basic Usage

Key Options

Read Type Options

Fast Mode

High-Quality Mode (PacBio HiFi)

Output Files

Wtdbg2 (Fast Draft)

Installation

Basic Usage

Platform Presets

Complete Workflows

ONT Bacterial Assembly

Hybrid Assembly (Long + Short)

Quality Expectations

Troubleshooting

Low Contiguity

Memory Issues

Misassemblies

Related Skills

How this skill was measured

Measured example — same prompt, with vs. without the skill · from the benchmark run · case case-15

Related skills