Name: Aleksei Korzhenkov
Type: User
Company: NRC Kurchatov Institute
Bio: 2018- research fellow at NRC Kurchatov Institute (Moscow, Russia).
2015-2018: jr. research fellow at
Microbial Genomics lab, IKBFU (Kaliningrad, Russia).
Location: Russia
Aleksei Korzhenkov's Projects
Simple scripts for bioinformatics
Conda recipes for the bioconda channel.
Kotlin realisation of bioinformatics routine operations and file handling.
SHort course on genome assembly and annotation
CWL tool to extract eukaryotic rRNA from genome assembly
DDBJ Fast Annotation and Submission Tool
Statistical anomalies in Russian elections
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
Express Phylogenetic Inference based on Multiple Markers
Fast Whole-Genome Similarity (ANI) Estimation
Visualization for genomics
GraftM additional packages
Mapping file generator for QIIME
Repository to host tool-specific module files for the Nextflow DSL2 community!
:zap: :aquarius: Rapid prokaryotic genome annotation
Protein hint generation pipeline for gene finding in eukaryotic genomes
Express metagenome binning
Source code and data relating to "SNP-based analysis reveals authenticity and genetic similarity of Russian indigenous grape cultivars" article
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.
hybrid assembly pipeline for bacterial genomes
YAMB: Yet Another Metagenome Binner
ZGA prokaryotic genome assembly and annotation pipeline