DeNovo approaches
Biotechvana is glad to offer data analysis services for different approaches “de novo” including assembly and annotation of both prokaryotic and eukaryotic genomes and transcriptomes without available reference, as well as WGS Metagenomics and Metatranscriptomics.
We also offer services for viruses and mobile elements full-length genome characterization or exhaustive characterization of the complete population of mobile genetic elements or viruses (mobilome or viriome) of a host or a sample. Although each study needs to be personalized depending on your experiment and the species to be characterized below we summarize the usual workflow followed by us in these types of studies.
Genomes, Transcriptomes, Metagenomes, Metatranscriptomes
1) Preprocessing of raw data
- Quality analysis of raw sequence data files (sff, fastq, sam, fasta, etc).
- Preprocessing of reads including demultiplex and removing of low-quality sequences, primers/adapter remnants and artifacts
and (when appropriate) trimming/clipping, of reads.
2) De Novo Assembly and scaffolding
- De Novo Assembly of processed reads (into contigs) and scaffolding
- Gap filling and re-scaffolding (in genome approaches)
- Reconstruction of the reference consensus assembly by merging two or more assemblies when needed
- Reconstruction of isoforms (in transcriptome approaches)
- Prediction and extraction of ORFs (only prokaryotes) or prediction of gene intron-exon structure (only eukaryotes)
- Inference of Assembly metrics
3) Annotation and functional analysis
- Repeat masking
- Automatic annotation of coding and non-coding genes
- Functional analysis and characterization of metabolic pathways
- Detection of features start-stop codons, promoters, etc
- Data integration
4) Downstream analyses
- Homo-polymer and frameshiftings correction on coding sequences
- Characterization of paralogs/orthologs
- Phylome annotation
- Mining and Knowledge discovery
- Comparative analysis
- Postprocessing and curation
- Implementation of databases
Full-length Genome Characterization of Virus and Mobile Genetic Elements
1) Preprocessing of raw data
- Quality analysis of raw sequence data files (sff, fastq, sam, fasta, etc).
- Preprocessing of reads including demultiplex and removing of low-quality sequences, primers/adapter remnants and artifacts
and when appropriate trimming/clipping, of reads.
2) De Novo Assembly
- De Novo Assembly of processed reads
- Circularization if appropriate
- Inference of Assembly metrics
3) Annotation
- Characterization of LTRs and TIRs if appropriate
- Annotation of ORFs for genes and other features.
- Phylogenetic analysis
Viriome/Mobilome annotation
1) Mapping and Annotation
- Repeat masking of repeats and transposons by comparative analysis against diverse reference databases.
- De Novo identification of repeats by self-comparison of the whole genome.
- Searching the genome for tandem repeats.
- Characterization of tight junctions.
- Characterization of LTRs and TIRs.
- Annotation of ORFs for genes and other features.
- Functional analysis using biological vocabularies such as Gene Ontology (GO).
- Characterization of metabolic pathways
- Phylome annotation and reconstruction
2) Integration and downstream analyses
- Full-length genome transposon reconstruction.
- Analysis of Orthologs
- Differential insertion analysis.
- Data integration and statistics analysis.
If you are interested in getting more information about our services for analysis of DeNovoSeq data, please contact us at biotechvana(at)biotechvana.com and we will be glad to pass you on a quote or organize a personalized meeting with you in order to discuss and evaluate your experiment.
