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koncevojdanila10-source/README.md

Hi, I'm Danial Kontsevoy

Data Scientist & Bioinformatician at National Laboratory Astana. MSc in Molecular Biotechnology & Biomedicine, L.N. Gumilyov Eurasian National University.

I build reproducible bioinformatics pipelines where every reported number is parsed from the pipeline's own output, and limits and negative results are stated openly.

Projects

RNA-seq-Best-Practice: human RNA-seq on chr19, from alignment to cis-eQTL; found a sample-identity conflict in published data.

-GATK_BEST_PRACTICE-: chrY and mtDNA variant calling and haplogroup assignment, cross-validated by two tools.

de_nova: Vibrio cholerae assembly from Illumina + Nanopore, four strategies compared.

ssu-rrna-tree-of-life: maximum-likelihood tree of life from SSU rRNA, IQ-TREE vs FastTree.

ecoli-wgs-mapping-qc and yeast-rnaseq-mapping-qc: mapping and QC pipelines.

AudioMind

I also built AudioMind, a Chrome extension that turns lectures into study notes: https://chromewebstore.google.com/detail/nflejmjkkehdgiginniiboagibdoemcd

Contact

LinkedIn: https://www.linkedin.com/in/danial-kontsevoy-b1728b393/

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  1. -GATK_BEST_PRACTICE- -GATK_BEST_PRACTICE- Public

    GATK Best Practices variant calling on human chrY and mtDNA, ending in paternal and maternal haplogroup assignment cross-validated by two independent tools. Reproduces published metrics to within 0…

    HTML

  2. de_nova de_nova Public

    De novo genome assembly pipeline (Illumina + Nanopore)

    Shell

  3. ecoli-wgs-mapping-qc ecoli-wgs-mapping-qc Public

    Reproducible WGS read-mapping & QC pipeline for E. coli — bwa-mem2, Picard, mosdepth, Qualimap, MultiQC

    HTML

  4. RNA-seq-Best-Practice RNA-seq-Best-Practice Public

    A complete human RNA-seq pipeline restricted to chr19 — alignment, quantification, variant calling, ASE and cis-eQTL — run end to end on 12 public PBMC libraries. Strandedness measured, three count…

    Shell

  5. ssu-rrna-tree-of-life ssu-rrna-tree-of-life Public

    Reproducible phylogenetics pipeline: 10-organism SSU rRNA tree of life (MAFFT, ClipKIT, IQ-TREE, FastTree) with a cross-check of the two tree builders.

    Shell

  6. yeast-rnaseq-mapping-qc yeast-rnaseq-mapping-qc Public

    Reproducible RNA-seq alignment & QC pipeline for S. cerevisiae — HISAT2, RSeQC, Qualimap, MultiQC

    HTML