Module Genome Analysis
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.
Genome Analysis use case: https://www.biobam.com/genome-assembly-annotation-sarocladium-oryzae/ .
Genome Analysis Example Dataset: Download.