OmicsBox Genome Analysis Module

The OmicsBox Genome Analysis Module is a comprehensive bioinformatics solution developed by BioBam that enables researchers to characterize and analyze newly sequenced genomes, taking projects from raw reads all the way through to fully annotated gene structures. Designed to be both efficient and user-friendly, the module supports eukaryotic, prokaryotic, and long-read genome analysis workflows, and runs out of the box on any standard PC or laptop running Windows, Linux, or macOS — with no specialized hardware requirements.

The module integrates a wide range of established bioinformatics tools into a single, cohesive interface, allowing researchers to perform de novo assembly, repeat masking, gene prediction, alignment, polishing, quality control, and exploratory analysis without switching between disparate software environments.

Quality Control and Assessment

• Perform quality control of sequencing samples using FastQC and Trimmomatic to filter reads and remove low-quality bases.
• Evaluate genome assembly quality and reliability using QUAST, which enables comparison of multiple de novo assembly strategies across key metrics including contiguity, completeness, accuracy, and fragmentation.
• Assess genome assembly completeness using BUSCO to ensure high-quality results before downstream analysis.

De Novo Genome Assembly

• Reconstruct whole genome sequences without a reference genome using three supported assembly algorithms: ABySS 2, SPAdes, and Flye.
• Supports both short-read and long-read sequencing technologies, providing flexibility across different experimental setups.
• Generate genome drafts for eukaryotic species by assembling DNA-Seq reads without additional prior information.
• Assemble and characterize prokaryotic genomes in a fast and sensitive manner, with the option to proceed to functional annotation of resulting gene sequences.
• For long-read workflows, assemble DNA-Seq long reads with Flye and use short reads to polish contigs with BWA and Pilon.

Alignment and Polishing

• Align short sequencing reads against large reference sequences using BWA or Bowtie 2.
• Correct and polish draft assemblies derived from long reads using Pilon.

Repeat Masking and Gene Finding

• Mask repetitive sequences in genome assemblies using RepeatMasker to improve the accuracy of downstream gene predictions.
• Perform eukaryotic gene predictions with Augustus, with the option to improve predictions by incorporating RNA-Seq data.
• Carry out prokaryotic gene finding using Glimmer to characterize genome structure in bacterial and other prokaryotic organisms.

Multi-Locus Sequence Typing (MLST)

• Unambiguously characterize bacterial isolates using MLST methodology.
• The procedure considers alleles present in typically seven well-characterized housekeeping genes, providing reliable strain identification.

Genome Browser and Visualization

• Visualize genome annotations as tracks in a side-scrolling genome browser, combining genome sequences (.fasta), alignments (.bam), intron-exon structures (.gff), and variant data (.vcf) in a unified view.
• Select and display specific genes directly from annotation tables within the interface.

Exploratory Analysis and Statistics

• Process large genome annotations through a rich user interface that supports filtering, sorting, and combining gene annotation datasets in General Feature Format (GFF) style.
• Access a variety of statistical charts and reports to evaluate genome assembly and characterization processes, supporting biological interpretation of results.

The OmicsBox Genome Analysis Module supports end-to-end genomic workflows for eukaryotic, prokaryotic, and long-read sequencing projects. It is compatible with Windows, Linux, and macOS on standard hardware, and is available via a free trial or custom demo for teams looking to streamline their genomics research pipeline.