Dataset Overview

This dataset contains all next-generation sequencing (NGS) data generated to evaluate the OMEGA gene assembly method. It includes PacBio HiFi long-read sequencing (BAM), Illumina paired-end sequencing (FASTQ), and Oxford Nanopore long-read sequencing (FASTQ). These data measure gene assembly accuracy, library composition, and functional screening of GFP variants.

All files contain DNA sequence reads. No processed tables or derived variables are included.

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Data Organization

The dataset is organized by sequencing platform and experiment type:

• PacBio HiFi (BAM): full-length assembled genes
• Illumina (FASTQ): short-read validation
• Oxford Nanopore (FASTQ): long-read variant analysis and sorted populations

Each filename encodes:

• library type (e.g., GFP, Rubisco)
• replicate number (rep1, rep2)
• sample type (presort, sorted bin, control)

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Key Definitions

• Presort: unsorted gene library before selection
• FACS: sorting of GFP variants by fluorescence
• GFP1–GFP5: increasing fluorescence bins (GFP1 = lowest, GFP5 = highest)
• N1, N2: negative gates
• NEG: combined negative population
• PreSort: unsorted Nanopore sample
• Replicate: independent experiment

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File Types

FASTQ (.fastq.gz)

Raw sequencing reads:

• nucleotide sequence (A, T, C, G)
• quality scores (Phred scale)

Units:

• sequence length: base pairs (bp)
• quality: Phred score

BAM (.bam)

Aligned long reads with metadata.

Associated files:

• .pbi: index
• .xml: metadata
• .md5sum: integrity check

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Data File Inventory

PacBio HiFi — Rubisco and Cas9

• lib1-hifi_reads.bam
• lib1-hifi_reads.bam.pbi
• lib2-hifi_reads.bam
• lib2-hifi_reads.bam.pbi

Illumina — PCR

• pcrs_R1.fastq.gz
• pcrs_R2.fastq.gz

Illumina — JSCAN

• jscan_R1.fastq.gz
• jscan_R2.fastq.gz

Oxford Nanopore — fscan

• fscan_ont_data.fq.gz

PacBio HiFi — Uniprot GFP

• uniprot_rep1_presort.bam
• uniprot_rep1_presort.bam.pbi
• uniprot_rep1_presort.bam.md5sum
• uniprot_rep1_presort.consensusreadset.xml
• uniprot_rep2_presort.bam
• uniprot_rep2_presort.bam.pbi
• uniprot_rep2_presort.bam.md5sum
• uniprot_rep2_presort.consensusreadset.xml

PacBio HiFi — SynGFP (Original)

• syngfp_rep1_presort.bam
• syngfp_rep1_presort.bam.pbi
• syngfp_rep1_presort.bam.md5sum
• syngfp_rep1_presort.consensusreadset.xml
• syngfp_rep2_presort.bam
• syngfp_rep2_presort.bam.pbi
• syngfp_rep2_presort.bam.md5sum
• syngfp_rep2_presort.consensusreadset.xml

PacBio HiFi — SynGFP (Repeat Assembly)

• syngfp_assembly2_rep1_presort.bam
• syngfp_assembly2_rep1_presort.bam.pbi
• syngfp_assembly2_rep1_presort.md5sum
• syngfp_assembly2_rep1_presort.consensusreadset.xml
• syngfp_assembly2_rep2_presort.bam
• syngfp_assembly2_rep2_presort.bam.pbi
• syngfp_assembly2_rep2_presort.md5sum
• syngfp_assembly2_rep2_presort.consensusreadset.xml

Oxford Nanopore — FACS GFP (Replicate 1)

• syngfp_rep1_GFP1.fq.gz
• syngfp_rep1_GFP2.fq.gz
• syngfp_rep1_GFP3.fq.gz
• syngfp_rep1_GFP4.fq.gz
• syngfp_rep1_GFP5.fq.gz
• syngfp_rep1_N1.fq.gz
• syngfp_rep1_N2.fq.gz
• syngfp_rep1_NEG.fq.gz
• syngfp_rep1_PreSort.fq.gz

Oxford Nanopore — FACS GFP (Replicate 2)

• syngfp_rep2_GFP1.fq.gz
• syngfp_rep2_GFP2.fq.gz
• syngfp_rep2_GFP3.fq.gz
• syngfp_rep2_GFP4.fq.gz
• syngfp_rep2_GFP5.fq.gz
• syngfp_rep2_N1.fq.gz
• syngfp_rep2_N2.fq.gz
• syngfp_rep2_NEG.fq.gz
• syngfp_rep2_PreSort.fq.gz

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Usage Notes

Viewing BAM files (PacBio HiFi)

Use samtools to inspect BAM files:

samtools view file.bam | head

Viewing FASTQ files (Illumina and ONT)

View reads directly:

zcat file.fastq.gz | head

Companion files

• .bam.pbi — PacBio index (not required for viewing)
• .consensusreadset.xml — metadata (not required for viewing)
• .md5sum — file integrity check (run: md5sum -c filename.md5sum)

Only .bam and .fastq.gz files are needed for basic inspection.

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Reuse

Applications include:

• gene assembly benchmarking
• variant reconstruction
• sequence–function modeling
• machine learning training datasets

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Ethical and Legal

• No human data
• Non-pathogenic sequences
• No restrictions on reuse (CC0)