Four new pipelines to streamline and improve genomic analyses

As part of its scope, G3 Genes|Genomes|Genetics is dedicated to reporting new methods and technologies of significant benefit to the genetics community. Here, we highlight a selection of new analysis pipelines and software developments from the August 2024 issue that promise to improve research and practical applications in their respective subfields. These advances include easy and ready-to-use genomics tools that improve data management and analysis and overcome long-time challenges, emphasizing the ongoing progress and innovation happening in genomics.

An easy-to-use phylogenetic analysis pipeline

A new turn-key pipeline called OrthoPhyl has answered the call to improve the phylogenetic analysis of bacterial genomes. Developed by Middlebrook et al., OrthoPhyl can analyze up to 1,200 input genomes and reconstruct high-resolution phylogenetic trees based on whole genome codon alignments from diverse bacterial clades.

The beauty of OrthoPhyl is that it streamlines a usually complex, multi-step process requiring extensive bioinformatics expertise and computing resources into a multi-threaded tool that runs from a single command.

With more than 2 million publicly available bacterial genomes in NCBI’s GenBank database, OrthoPhyl can help research groups in the fields of bacterial phylogenetics and taxonomy take advantage of existing datasets to inform their ongoing analyses amid the ever-expanding sea of bacterial diversity.

Accurate genotype phasing and inference of grandparental haplotypes

To improve the analysis of complex plant genomes, Montero-Tena et al. have developed a new computational pipeline called haploMAGIC, which lets researchers identify locations of recombination known as genome-wide crossovers (COs) in multi-parent populations. haploMAGIC uses single-nucleotide polymorphism (SNP) data and known pedigree information to accurately phase genotypes, i.e., determine which alleles were inherited from each parent, and to reconstruct grandparental haplotypes, i.e., determine which alleles were inherited from each grandparent.

When tested on real-world data, haploMAGIC improved upon existing methods by using different levels of haploblock filtering to prevent false-positive COs—a common limitation—even as rates of genotyping errors increased. haploMAGIC can also distinguish between COs and gene conversions. By learning more about the position and frequency of genetic recombination events in complex plant genomes, breeders can better manage and expand genetic variation in their breeding programs.

A complete HiC/HiFi assembly pipeline

The USDA-ARS AgPest100 Initiative aims to create high-quality genome assemblies of pest insects that threaten agricultural production. However, the high cost and time currently needed to produce and manage these assemblies often hinders progress.

Molik et al. set out to address this challenge by developing a new Hi-C/high-fidelity (HiFi) sequencing genomic assembly pipeline called only the best (otb) using the Nextflow programming language. They then used otb to create a HiC/HiFi genome of the two-lined spittlebug, a significant agricultural pest that is not well understood. Overall, otb was able to streamline the process and reduce manual input and analysis time—including time spent organizing data and installing and calibrating bioinformatic tools.
By saving time, otb can significantly reduce costs for large genomic projects like AgPest100 and pave the way for new discoveries. Indeed, the HiC/HiFi assembly of the spittlebug genome represents a first step toward better understanding this plant-eating pest, which may lead to new, sustainable ways to manage it.

Assigning triploids to their diploid parents

Roche et al. have developed the first publicly-available, ready-to-use software for assigning triploid fish to their diploid parents. Triploidy means that an organism has three sets of chromosomes instead of two, and sterile triploids are commonly used in aquaculture breeding programs for their better yield and growth and to prevent genetic contamination of wild fish populations. The authors improve upon existing frameworks by updating the parentage assignment R package APIS to support triploids with diploid parentage.

When assessed with simulated and real datasets, APIS accurately assigned triploid offspring to their diploid parents using both likelihood and exclusion methods. The new software represents a key tool for establishing pedigrees in fish farming.