Microbial Omics Analyses
In Biotechvana we are glad to offer bioinformatics services for diversity analysis, assignation of taxonomy levels, and microbiota community comparison of fungal or bacterial metagenomic samples sequenced based on 16s/18s, and/or ITs amplicons. Although each study needs to be specified in the context of your experiment design, and the species, and/or sample in analysis, below we summarize the usual workflow followed by us in these types of studies.
1) Preprocessing of raw data
2) Resolution of OTU (Operative Taxonomical Units) or ASV (Amplicon Sequence Variants)
- 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.
3) Mapping and assignation of taxonomy levels
- Conversion from Fastq to fasta
- Elimination of artifacts, small size sequences.
- Cluster analysis for the definition of OTU/ASV.
- Quantification of OTU/ASV
4) Downstream analyses
- Alignment of OTU/ASV against the most common 16s/18s rRNA RefSeq databases.
- Alignment refinement when appropriate.
- Assignation of taxonomy levels (Domain, Phylum, Class, Order, Family, Genus) using bootstrapping threshold
- Inference of metrics
- Venn diagrams
- Rarefaction curves
- Diversity Indexes
- Phylogenetic analyses
- KRONA analyses
- Testing hypotheses
- Statistical analysis
If you are interested in getting more information about our services for analysis of microbial amplicon 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.