Data of WGS-based non-invasive prenatal testing (NIPT) or cell-free DNA testing contains exogenous DNA (bacterial and viral). This information is too fragmentary to conduct full microbiome studies, but still interesting for expanding NIPT functionality.
Being a retrovirus, HIV can not be directly detected in cell-free DNA data.
Steps of the study:

1. Extraction of unmapped reads
2. Assigning taxonomic labels
3. Creating residual virus and microbiome profiles of two datasets
4. Analysis of the HIV-positive sequencing data
5. Finding the differences in exogenous DNA composition between HIV- and HIV+ NIPT samples
   

• Skills: Bash, bowtie2, Snakemake, Kraken2, KrakenTools, MaAsLin2.
  

Performed genome-based safety assessment of the probiotic strain Lpb. plantarum IS-10506.
Determined the multivariate association between clinical metadata and microbial meta-omics characteristics in a clinical study comparing gut microbiota profiles in stunted and normal children aged 36-45 months.

• Skills: BAGEL4, CRISPRCasFinder, R, dplyr, ggplot2, tidyverse, tidyr, MaAsLin2.
  

1. SequenceForge-Lite
   Lightweight tool to work with biological sequences, providing various functionalities for filtering .fastq files and manipulating .fasta files

2. MyAwesomeEDA
   Python module that provides a set of tools for exploring and analyzing your dataset

Projects completed during training at the Bioinformatics Institute:

1. Variant calling of Escherichia coli WGS
2. Variant calling of deep sequencing data (Influenza A virus (H3N2) hemagglutinin gene)
3. De novo assembly of Escherichia coli genome (TBD)
4. Tardigrade Ramazzottius varieornatus genome annotation and protein function prediction
5. Genotyping and SNP annotation of human 23andMe data
6. RNA-seq data analysis for differential gene expression of Saccharomyces cerevisiae after 30 minutes of fermentation
7. Ancient metagenomes analysis examining human dental calculus
8. Annotation of the immune repertoire derived from the T-cell population in a relatively healthy donor
9. Single-cell CITE-seq analysis detailing the cellular composition and transcriptional profiles within human bone marrow

Manual on conducting studies within human microbiome. As an example, data on the composition of the gut microbiome in people with Crohn's disease and healthy controls are presented.

Handbook on conducting NGS data analysis studies. At the moment there are detailed manuals on Quality Control and Variant Calling along with the complete pipeline of simple research in phylogenetics. Much more to be disclosured soon!