Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

An assembly workflow for analysing data in the Earth Biogenome Project pilot project.

Topology weighting by iterative sampling of sub-trees

Tutorials on evolutionary genomics

General tools for genomic analyses.

Must-read papers on graph neural networks (GNN)

A collection of papers and resources about Data-centric Graph Machine Learning (DC-GML).

order a FASTA file by microchromosome specific genes

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

WinPCA. A package for windowed principal component analysis.

A curated list of awesome Bioinformatics libraries and software.

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is…

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

OpenGL Powered Pretext Contact Map Viewer

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

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Fast and accurate tool for estimating genomic distances between genome-skims

Program for analysing NGS data.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Reference-free profiling of polyploid genomes

SplitsTree App

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

Extensive de-novo TE Annotator

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

⛓ Correct misassemblies using linked AND long reads

Filter SAM file for soft and hard clipped alignments

Minimal but speedy quality control for nanopore reads in Rust 🐻

software tools for haplotype assembly from sequence data