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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.
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.
The assembly feature allows to reconstruct whole genome sequences without a reference genome or specific hardware requirements. Assemble sequencing data from several technologies with 2 different algorithms: ABySS and SPAdes.
Mask repeats and low complexity DNA sequences of your eukaryotic genome assemblies with RepeatMasker to improve downstream gene predictions.
Perform prokaryotic (Glimmer) and eukaryotic (Augustus) gene predictions to characterize genome structure. The eukaryotic gene prediction offers RNA-seq intron hint support.
- DNA-Seq de novo assembly with ABySS 2
- DNA-Seq de novo assembly with SPAdes
- Repeat masking with RepeatMasker
- Eukaryotic gene finding with Augustus
- Prokaryotic gene finding with Glimmer