busco

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs

scripts associated with yam genome assembly

Snakemake workflow to construct species phylogenies using BUSCOs

Reproducible phylogenomics pipeline that builds partitioned species trees from BUSCO v5 results.

A pipeline to construct phylogenetic tree using BUSCOs

This pipeline contains several scripts used to construct phylogenies using BUSCO single-copy proteins. It works directly from BUSCO outputs and can be used for supermatrix or supertree methods. Utility scripts are available to automate the process when several genomes are to be used.

Unified bacterial genome QC: BUSCO-style completeness, contamination detection that tells plasmids from contaminants, and comparative gene content with a permutation null for genomic islands.

phylogeny and collinearity aware assembly evaluation toolkit.

A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.

A modular Nextflow DSL2 pipeline for reproducible plant de novo genome and transcriptome assembly, quality control, validation, and functional analysis.