⚡ ♒ Rapid prokaryotic genome annotation

Trinity RNA-Seq de novo transcriptome assembly

Manage perl installations in your $HOME

✂️ ⚡ Rapid haploid variant calling and core genome alignment

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

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

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Rapid large-scale prokaryote pan genome analysis

TransDecoder source

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

STAR-Fusion codebase

Genome Assembly and Annotation Service code

De-Novo Repeat Discovery Tool

PASA software

🌳 Create a tree using Mash distances

Plugins for the Ensembl Variant Effect Predictor (VEP)

Biopieces is a bioinformatic framework of tools easily used and easily created.

Learning the Variant Call Format

Convert various sequence formats to FASTA

Learning the Sequence Alignment/Map format

MITObim - mitochondrial baiting and iterative mapping

source code for EVM

Long-read metagenomic analysis

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Tools for working with second gen assemblies, fasta sequences, etc

A tool for the spatial analysis of diversity

⛓ Long Interval Nucleotide K-mer Scaffolder