ack is a grep-like search tool optimized for source code.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Extensive de-novo TE Annotator

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

De-Novo Repeat Discovery Tool

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

VarDict

NOVOPlasty - The organelle assembler and heteroplasmy caller

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

Plugins for the Ensembl Variant Effect Predictor (VEP)

A toolbox for pangenome analysis and threshold evaluation.

Dfam Transposable Element Tools Docker container.

An accurate and ultra-fast hybrid genome assembler

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Filter SAM file for soft and hard clipped alignments

use long sequenced reads to close gaps in assemblies

Custom tools to 'facilitate' BioNano Genomics data analysis

A unified array job submitter for LSF, SGE/UGE and Slurm

Create a pseudohaploid assembly from a partially resolved diploid assembly

Evaluation of phasing performance

Conversion of a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

Converts snpeff annotations into MAF

Scripts used for whole genome analysis comparison (WGAC)