mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization

🌳 Human ancestry inference from genomic data

Tandem repeat expansion detection or genotyping from long-read alignments

Massively parallel phylogenetic placement of genetic sequences

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Implementation of ToL genome assembly workflows

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

Observe FastAPI app with three pillars of observability: Traces (Tempo), Metrics (Prometheus), Logs (Loki) on Grafana through OpenTelemetry and OpenMetrics.

FastAPI Tips by The FastAPI Expert!

Tools for managing natural variation collections

Quickly get coverage statistics given reads and an assembly

A comprehensive, opinionated plant variant calling pipeline in Snakemake

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Demonstration of speciation and descent from a common ancestor

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioin…

Identify conserved positions in amino acid multiple sequence alignments in R

Bioinformatics protocol that aims at mining information at the sequence and structure level of protein chain to detect possible evolutionary conserved residues.

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniP…

Construction and utility of BWT for DNA string sets

Materials for genome annotation sessions at the WORKSHOP ON GENOMICS, CESKY KRUMLOV

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

GeneMark-ETP: gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer

LongcallR is a small variant caller for single molecule long-read RNA-seq data

MarginPolish: Graph based assembly polishing

A genome completeness evaluation tool based on miniprot

A deep learning consensus polisher

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).