🧬 🍄 🌍 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.
- 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 summarizer (from sequences clustering with VSEARCH/USEARCH/SWARM)
- 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