The OmicsBox Genome Analysis module allows to characterize and analyze newly sequenced genomes, from raw reads to gene structures in an efficient and user-friendly way.
Use FastQC and Trimmomatic to perform the quality control of your samples, to filter reads and to remove low quality bases.
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.
Align short sequencing reads against large sequences with BWA, and correct draft assemblies from long reads with Pilon.
Mask repeats of genome assemblies with RepeatMasker to improve downstream gene predictions.
Perform prokaryotic (Glimmer) and eukaryotic (Augustus) gene predictions to characterize genome structure.