Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs

MOTIVATION

With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.

RESULTS

We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.

AVAILABILITY AND IMPLEMENTATION

Gfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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