⚡ ♒ Rapid prokaryotic genome annotation

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

Extensive de-novo TE Annotator

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

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

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

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

🌳 Create a tree using Mash distances

Application of pan-genome for population

Learning the Sequence Alignment/Map format

Long-read metagenomic analysis

simuG: a general-purpose genome simulator

Tools for the analysis of structural variation in genomes

⛓ Long Interval Nucleotide K-mer Scaffolder

Somatic copy number analysis using WGS paired end wholegenome sequencing

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

Graph-based mapping of long sequences, noisy or HiFi.

Filter SAM file for soft and hard clipped alignments

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Benchmark datasets for WGS analysis

Create a pseudohaploid assembly from a partially resolved diploid assembly

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

Get microbial sequence data easier and faster

Assembly based core genome SNP alignments for bacteria

Using k-mers to call HLA alleles in RNA sequencing data

Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.

Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context