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title: "Module Genome Analysis"
canonical: "https://help.biobam.com/space/OBD/597950596/Module%20Genome%20Analysis"
format: markdown
---
Figure 1:  Genome Analysis menu The OmicsBox Genome Analysis module allows to characterize and analyse 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, to filter reads, and to remove low-quality bases. De novo  Assembly : The assembly feature allows to reconstruct 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 ) gene predictions to characterize genome structure. The eukaryotic gene prediction offers RNA-seq intron hint support. Additional Resources Genome Analysis use case:   . Genome Analysis Example Dataset:  Download .