👋 Hi, I'm Vladimir Mikryukov

🧬 🍄 🌍 I'm a molecular ecologist passionate about biodiversity, metagenomics and ecological statistics.
I work as a Research Fellow at the Institute of Ecology and Earth Sciences at the University of Tartu.

Main programs

• NextITS [Nextflow, R, bash] - A pipeline for metabarcoding eukaryotes with full-length ITS sequenced with PacBio
• PhyloNext [Nextflow, R, Python] - A pipeline for phylogenetic diversity analysis of GBIF-mediated data and Open Tree of Life synthetic phylogenies
• phredsort [Go] - A cli tool for sorting sequences in a FASTQ file by their quality scores
• SeqHasher [Go] - A tool for hashing individual sequences in FASTA files
• symlink2file [Go] - A tool to replace symlinked files with their original files
• tshbot [Go] - Program for executing shell commands via Telegram
• goclust [Go] - Clustering tool for sparse matrices produced by USEARCH
• ucs [Go] - UC file proccessing tool (USEARCH/VSEARCH/SWARM cluster format)
• BatchBlaster [Nextflow] - A Nextflow-based pipeline for taxonomic classification (currently with BLAST)
• metagMisc [R] - Miscellaneous functions for metagenomic analysis
• SHMatcher [Nextflow, Python] - Species hypothesis (SH) matching analysis tool
• phylonest [R] - Equivalent numbers for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales
• nex2tbl [R] - Preparation of protein-coding DNA sequences for the submission to GenBank