RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Easily generate information-rich, publication-quality tables from R

Fast Whole-Genome Similarity (ANI) Estimation

EzAAI - High Throughput Prokaryotic AAI Calculator

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Islander - Greek islands from a Greek perspective

🔬 ♌ Bacterial ribosomal RNA predictor

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

Python programs for processing GFF3 files

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Using Deep Learning to predict gene annotations

tiara – a tool for DNA sequence classification

Interactive quality assessment of genome assemblies

Accurate and rapid RiboRNA sequences Detector based on deep learning

This is a template for all assembly projects. Please read the instructions below on how to use it.

TSEBRA: Transcript Selector for BRAKER

Step-by-step tutorial to create synteny plots for pairs and trios of genomes using JCVI's MCScan

TELR is a fast non-reference transposable element detector from long read sequencing data.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact o…

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…

An accurate GFF3/GTF lift over pipeline

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

🔬 Assemble large genomes using short reads

Identify and find telomeres, or telomeric repeats in a genome.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A set of workflows written in Nextflow for Genome Annotation.

Saccharomyces transposable element canonical sequences

📈😻 Emoji in ggplot2 😻📈