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.
Visualize your annotations in form of tracks to combine the genome sequences (.fasta) with alignments (.bam), intron-exon structure (.gff) and variant data (.vcf).
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.
Mask repeats of genome assemblies with RepeatMasker to improve downstream gene predictions.
Perform prokaryotic (Glimmer) and eukaryotic (Augustus) gene predictions to characterize genome structure.
Align short sequencing reads against large sequences with BWA or Bowtie 2, and correct draft assemblies from long reads with Pilon.
Characterize bacterial isolates unambiguously. This procedure considers the alleles present in (usually) seven well-characterized housekeeping genes.