Data Pre-processing

Quality Control (QC):

Assess raw sequencing data's quality (QC) to identify and remove low-quality and bad reads.

Adapter and Contaminant Removal:

Trim or filter sequences to remove adapters and contaminants. The obtained reads will be used for the downstream analysis pipeline.

Host or Chloroplast/ Mitochondrial Contaminants Removal (optional upon request):

If analyzing a host-associated microbiome, remove host DNA or RNA sequences to focus on primarily microbial content using the QIIME 2 pipeline.

Taxonomic Profiling:

Identify and calculate the taxonomic composition of the microbial community.

Designate sequences for taxonomic groups using tools like BLAST or Krake,.

Visualize taxonomic profiles through plots like bar charts, stacked histograms or heatmaps.

Diversity Analysis (Basic and advanced):

Calculate alpha diversity (within-sample diversity) and beta diversity (between-sample diversity) metrics to understand microbial diversity and community structure.

Generate diversity plots and ordination techniques (e.g., PCoA or NMDS) to visualize diversity patterns.

Statistical Analysis:

Perform statistical tests to identify significant differences in taxonomic or functional profiles between sample groups, such as treatment and control groups.

Assembly (optional and for additional charges):

If working with metagenomic data without reference genomes, Assemble short reads into contigs to reconstruct draft genomes of individual microorganisms. We use tools like SPAdes or MEGAHIT can be used for metagenomic assembly.

Metagenomic Binning (optional and for additional charges):

Group contigs or sequences into bins representing individual microbial genomes. We use tools like CONCOCT, MaxBin, or MetaBAT can assist in metagenomic binning.

Network Analysis (optional and for additional charges):

Construct ecological networks to understand interactions between different microbial taxa within a community.

Functional Annotation:

Assess the functional potential of the microbial community by annotating genes and pathways. There are different pipelines for bacteria and fungi (16S and ITS).

MG-RAST, IMG/M, or KEGG can predict functional genes and pathways.

Visualize functional profiles through heatmaps and functional enrichment dot plots.

Functional and Taxonomic Profiling at the Genome Level(optional):

Annotate genes within metagenomic bins to gain insights into the functional potential and taxonomic identity of individual microbial genomes.

Visualization and Interpretation:

Visualize the results of taxonomic profiling, functional annotation, diversity analysis, and any other relevant analyses.

Interpret findings to gain insights into the structure, function, and ecological dynamics of the microbial community. (upon special request and additional charges)

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We offer custom analysis pipelines based on clients' requirements.

Special discounts available on large datasets.

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