16s/18s Metagenome analysis
Biotechvana offers bioinformatic services for diversity analysis, assignation of taxonomy levels and microbiota community comparison of fungal or bacterial metagenomic samples sequenced based on 16s/18s 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 this type of studies.
1) Preprocessing of raw data
2) Mapping and assignation of taxonomy levels
- 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 appropiate) trimming/clipping, of reads.
3) Phylogenetic analyses
- Alignment of raw reads over the most common 16s/18s rRNA RefSeq databases.
- Alignment refinement and core definition.
- Elimination of artifacts, small size sequences and redundancy.
- Assignation of taxonomy levels (Domain, Phylum, Class, Order, Family, Genus) using bootstrapping threshold
- Inference of metrics
4) Downstream and diversity analyses
- OTUs definition by cluster analysis.
- Venn Diagrams
- Rarefaction curves
- Diversity Indexes
- Statistical analysis