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Module Genome Analysis

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The OmicsBox Genome Analysis module allows the characterization and analysis of newly sequenced genomes, from raw reads to gene structures in an efficient and user-friendly way.

  • **Quality Control and Assessment:**Use FastQC and Trimmomatic to perform the quality control of your samples, and filter reads, and to remove low-quality bases.
  • De novoAssembly: The assembly feature allows the reconstruction of whole-genome sequences without a reference genome or specific hardware requirements. Assemble sequencing data from both, short and long-read technologies with 3 different algorithms: ABySS, SPAdes, and Flye.
  • **Alignment and Polishing:**Align short sequencing reads against large sequences with BWA, and correct draft assemblies from long-reads with Pilon.
  • **Repeat Masking:**Mask repeats and low-complexity DNA sequences of your eukaryotic genome assemblies with RepeatMasker to improve downstream gene predictions.
  • **Gene Finding:**Perform prokaryotic (Glimmer) and eukaryotic (AUGUSTUS and EviAnn) gene predictions to characterize genome structure. AUGUSTUS offers RNA-seq intron hint support, and EviAnn builds gene models from transcript and protein evidence.

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image-20240430-143626.png Additional Resources

Genome Analysis use case: Genome Assembly Annotation Sarocladium Oryzae.

Genome Analysis Example Dataset: Download.