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mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization
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.
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
rrwick / pypolca
Forked from gbouras13/pypolcaStandalone 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…
Materials for genome annotation sessions at the WORKSHOP ON GENOMICS, CESKY KRUMLOV
KatharinaHoff / teaching
Forked from bpucker/teachingThis 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
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).