https://github.com/vmikk/vmikk
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https://github.com/vmikk/vmikk
Last synced: 6 months ago
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Profile
- Host: GitHub
- URL: https://github.com/vmikk/vmikk
- Owner: vmikk
- Created: 2024-06-18T10:32:33.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-12T19:37:38.000Z (11 months ago)
- Last Synced: 2025-03-24T20:14:40.399Z (10 months ago)
- Size: 4.88 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
### 👋 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](https://github.com/vmikk/NextITS) [Nextflow, R, bash] - A pipeline for metabarcoding eukaryotes with full-length ITS sequenced with PacBio
- [PhyloNext](https://github.com/vmikk/PhyloNext) [Nextflow, R, Python] - A pipeline for phylogenetic diversity analysis of GBIF-mediated data and Open Tree of Life synthetic phylogenies
- [phredsort](https://github.com/vmikk/phredsort) [Go] - A cli tool for sorting sequences in a FASTQ file by their quality scores
- [SeqHasher](https://github.com/vmikk/SeqHasher) [Go] - A tool for hashing individual sequences in FASTA files
- [symlink2file](https://github.com/vmikk/symlink2file) [Go] - A tool to replace symlinked files with their original files
- [tshbot](https://github.com/vmikk/tshbot) [Go] - Program for executing shell commands via Telegram
- [goclust](https://github.com/vmikk/goclust) [Go] - Clustering tool for sparse matrices produced by USEARCH
- [ucs](https://github.com/vmikk/ucs) [Go] - UC file proccessing tool (USEARCH/VSEARCH/SWARM cluster format)
- [BatchBlaster](https://github.com/vmikk/BatchBlaster) [Nextflow] - A Nextflow-based pipeline for taxonomic classification (currently with BLAST)
- [metagMisc](https://github.com/vmikk/metagMisc) [R] - Miscellaneous functions for metagenomic analysis
- [SHMatcher](https://github.com/vmikk/SHMatcher) [Nextflow, Python] - Species hypothesis (SH) matching analysis tool
- [phylonest](https://github.com/vmikk/phylonest) [R] - Equivalent numbers for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales
- [nex2tbl](https://github.com/Mycology-Microbiology-Center/nex2tbl) [R] - Preparation of protein-coding DNA sequences for the submission to GenBank