✂️ ⚡ Rapid haploid variant calling and core genome alignment

Extensive de-novo TE Annotator

Any Way to Show Multi genomic Synteny

Genome Assembly and Annotation Service code

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.

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

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

GATB Minia assembly pipeline

scripts to parse and analyse MCScanX collinearity output

A box of genomics tools

Workflows I find helpful for fungal genome annotation

parallelLastz: Running Lastz in parallel

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

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