busco

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

A Nextflow pipeline for evaluating assembly quality

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

A nextflow pipeline for polishing CLR assemblies

Assembly of Nanopore Sequencing

A tool to filter BUSCO output into single-copy gene files for phylogenomics

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.

Run Assembly statistics on a genome assembly (BUSCO and assemblyStats and new_Assemblathon.pl)

Making BUSCO HMMs useable in Anvi'o.

A pipeline to construct phylogenetic tree using BUSCOs

Building a fully automized pipeline for phylogenomic analyses based on the BUSCO toolkit

A comparative annotation toolkit (CAT) pipeline for 301 Drosophila genomes.

A transparent ONT bacterial assembly case study for an *Acinetobacter* barcode07 isolate, built not only to generate an assembly, but to show how raw reads become an interpretable genome through QC evidence, assembler comparison, graph checks, phylogeny, annotation, documented decisions, and honest limitations.

Create a SNAP model from BUSCO output

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.

End-to-end Pseudomonas carnis WGS pipeline for genome assembly, QC, read mapping, AMR, plasmid & virulence profiling.

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.

phylogeny and collinearity aware assembly evaluation toolkit.