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CompBioBench item

gene-fusion-q2

Question

You are given a bulk RNA sequencing FASTQ file (gene.fusion.q2.fq.gz) from human. The data contains a synthetic gene that is a fusion of multiple genes. Your task is to identify the genes whose exons make up the fusion gene. Report the answer as the names of the genes joined by a hyphen, in 5' to 3' order, for each exon, written in all uppercase letters, HGNC symbols. For example: TCF21-COL1A1-FN1

Inferred answer
MYC-SP1-ZIC2-SP1-CATSPER4Uniquely inferred from submitted scores.
Domain
Transcriptomics
Question style
Synthetic/Augmented Data

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

CorrectUDT-only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Fusion diagnostic kmer scanFusion ordered split read scanFusion split component assembly
Total tokens
882.1K
Output
16.0K
Codex GPT-5.5

Replicate 2

CorrectUDT + standard tools
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Fusion junction kmer diagnosticFusion junction kmer diagnostic v2Fusion junction render probe v3UDT render probeNcbi Blastn Wrapper
Total tokens
2.5M
Output
19.3K
Codex GPT-5.5

Replicate 3

CorrectUDT + standard tools
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Fastq StatsTrinitySummarize Trinity Fusion AssemblySummarize Trinity Fusion Assembly v2Fasta Compute Length6 more tools
Total tokens
3.9M
Output
18.3K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

CorrectUDT + standard tools
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
FastqcRnaspadesFasta Compute LengthTp Sort Header ToolMinimap25 more tools
Total tokens
8.9M
Output
19.2K
Codex GPT-5.6 Sol

Replicate 2

CorrectUDT + standard tools
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
FastqcRnaspadesFasta StatsNcbi MakeblastdbFusion candidate scan against GENCODE v495 more tools
Total tokens
11.6M
Output
25.9K
Codex GPT-5.6 Sol

Replicate 3

CorrectUDT + standard tools
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
FastqcTrinitySalmonSort rowsNcbi Blastn Wrapper11 more tools
Total tokens
54.4M
Output
58.3K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

CorrectStandard tools only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
No Galaxy tool job recorded
Total tokens
36.2M
Output
79.5K
Codex + DeepSeek-v4-pro-0813

Replicate 2

CorrectStandard tools only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
RnaspadesFasta Compute LengthFasta Filter By LengthNcbi Blastn WrapperNcbi Makeblastdb2 more tools
Total tokens
13.8M
Output
55.2K
Codex + DeepSeek-v4-pro-0813

Replicate 3

CorrectStandard tools only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Fastq StatsRnaspadesFasta StatsTrinityFasta Filter By Length6 more tools
Total tokens
8.5M
Output
42.8K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

CorrectStandard tools only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
FastqcTrinityFasta Compute LengthFasta Filter By LengthNcbi Blastn Wrapper3 more tools
Total tokens
21.4M
Output
44.5K
Codex GPT-5.6 Luna

Replicate 2

CorrectStandard tools only
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Fastq StatsTrinityFasta Filter By LengthNcbi Blastn Wrapper
Total tokens
44.7M
Output
79.4K
Codex GPT-5.6 Luna

Replicate 3

IncorrectStandard tools only
AnswerTPM3-MT-ATP6-MT-CO3
Workflow
Fastq StatsFastqcTrinityFasta Filter By LengthNcbi Blastn Wrapper
Total tokens
33.1M
Output
86.7K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Incorrect
AnswerMYC-SP1-CATSPER4
Workflow
Local codeMinimap2Bowtie2BLASTNPython3 more tools
Codex GPT-5.5

Replicate 2

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools2 more tools
Codex GPT-5.5

Replicate 3

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeBWA-MEMBowtie2Minimap2BLASTN2 more tools

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools
Codex GPT-5.6 Sol

Replicate 2

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codePythonBWA-MEMBowtie2Minimap22 more tools
Codex GPT-5.6 Sol

Replicate 3

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools2 more tools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Incorrect
AnswerMYC-SP1-CATSPER4
Workflow
Local codePythonSamtoolsMinimap2Bowtie23 more tools
Total tokens
9.1M
Output
72.1K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codePythonSamtoolsBWA-MEMMinimap24 more tools
Total tokens
8.8M
Output
69.2K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeBWA-MEMMinimap2Bowtie2Samtools4 more tools
Total tokens
5.5M
Output
44.6K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMSamtoolsBLASTN1 more tools
Codex GPT-5.6 Luna

Replicate 2

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMBowtie2BLASTN4 more tools
Codex GPT-5.6 Luna

Replicate 3

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools3 more tools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Correct
AnswerMYC-SP1-ZIC2-SP1-CATSPER4
Workflow
Local codePythonBLASTNMinimap2Samtools
Total tokens
381.2K
Output
4.5K