A tool for evaluating long-read de novo assembly results

Whole Genome Alignment Tools

Reorients assembled microbial sequences

TGSFilter: An ultra-fast and efficient tool for long reads filtering and trimming

Python Redmine is a library for communicating with a Redmine project management application

A genome browser designed for complex structural variants and long reads.

GFA visualizer, GPU-accelerated using Vulkan

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Genome Annotation Pipeline

This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.

Material for the Reference Graph Pangenome Data Analysis Hackathon 2023, November 13-17 in Cape Town, South Africa

Given a file of marker locations in one genome, report the locations of those markers in a second genome.

A DSL for data-driven computational pipelines

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Pan gGnome Viewer

Everything is bigger in Texas: Pan-Structural Variation hackathon in the Cloud!

A VCF comparison engine for structual variant benchmarking

Program for aligning DNA sequences, a pairwise aligner.

Write a Collaborating Authors table suitable for USDA/NSF COA/COI files

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

Hidden Markov Model based Copy number caller

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:

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