asan-emirsaleh

tama

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

fastapi-observability

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

fastapi-tips

FastAPI Tips by The FastAPI Expert!

NVTK

Tools for managing natural variation collections

Koverage

Quickly get coverage statistics given reads and an assembly

Acanthophis

A comprehensive, opinionated plant variant calling pipeline in Snakemake

pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Bugraft

Demonstration of speciation and descent from a common ancestor

pypolca

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

FluentDNA

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 bioinformatics projects.

ConPosER

Identify conserved positions in amino acid multiple sequence alignments in R

ResidueFisher

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

Annocript

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, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript

ropebwt3

Construction and utility of BWT for DNA string sets

GenomeAnnotation_Workshop

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

teaching

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

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

NeuralPolish

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

BlockPolish

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

longcallR

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

MarginPolish

MarginPolish: Graph based assembly polishing

compleasm

A genome completeness evaluation tool based on miniprot

roko

A deep learning consensus polisher

herro

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).

AFFiNE

There can be more than Notion and Miro. AFFiNE(pronounced [ə‘fain]) is a next-gen knowledge base that brings planning, sorting and creating all together. Privacy first, open-source, customizable and ready to use.

Snaketool

Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff

ntsm

This tools counts the number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to compute the probability that sample are of the same origin to discover incongruent samples or sample swaps.

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

obsidian-semantic-canvas-plugin