✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Extensive de-novo TE Annotator

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.

Genome Assembly and Annotation Service code

Any Way to Show Multi genomic Synteny

NOVOPlasty - The organelle assembler and heteroplasmy caller

MITObim - mitochondrial baiting and iterative mapping

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

⛓ Long Interval Nucleotide K-mer Scaffolder

my bin directory

Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing

scripts to parse and analyse MCScanX collinearity output

GATB Minia assembly pipeline

Workflows I find helpful for fungal genome annotation

A box of genomics tools

Pipeline used to test for an enrichment of sweeps in a set of genes while controlling for confounding factors and with the option to run a full FDR analysis by using randomized genomes. See the ava…

A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes

parallelLastz: Running Lastz in parallel

Genome annotation pipeline v2

Phylogenomics tutorial based on BUSCO genes

Scripts used to reformat typical sequence data files such as fasta files and gff files.

detect Allelic Contigs by Shared Gene Content