# Mapler: Assessing assembly quality in taxonomically-rich metagenomes sequenced with HiFi reads

Nicolas Maurice, Clémence Frioux, Claire Lemaitre, Riccardo Vicedomini

► To cite this version:

Nicolas Maurice, Clémence Frioux, Claire Lemaitre, Riccardo Vicedomini. Mapler: Assessing assembly quality in taxonomically-rich metagenomes sequenced with HiFi reads. 2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France., pp.1-1, 2025. hal-04941137

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Submitted on 11 Feb 2025

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# Mapler: Assessing assembly quality in taxonomically-rich metagenomes sequenced with HiFi reads

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Nicolas Maurice¹,², Clémence Frioux², Claire Lemaitre¹, Riccardo Vicedomini¹,

¹ Inria/IRISA Genscale, Campus de Beaulieu, 35042 Rennes, France; ² Inria/INRAE Pleiade, Campus de Talence, 33405 Bordeaux, France
nicolas.maurice@inria.fr

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Université
de Rennes

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UNIR
IRISA

## Introduction

### Plant microbiomes

Plants recruit their microbiomes from millions (10³-10⁸/g) of soil micro-organisms, to regulate key functions such as [1]:

* Nutrition and growth,

* Abiotic stress,

* Biotic stress.

Yet, those taxonomically-rich ecosystems are poorly characterised. It is unclear how much of the improvements in sequencing and assembly scale to those complex ecosystems.

### Metagenome evaluation

In taxonomically-rich ecosystems, metagenome evaluation is a challenging task [2], due to:

* Low quality assemblies

* A lack of references databases

We present Mapler, a metagenome assembly and evaluation pipeline for HiFi reads in taxonomically-rich ecosystems.

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## How to evaluate the low-quality metagenome assemblies in soil and plant microbiomes ?

## Software description

### Overview

Mapler assembles, bins and evaluate multiple samples in parallel locally or on a cluster. After downloading it and snakemake, it installs dependencies itself.

It can be found in an upcoming paper and at :

gitlab.inria.fr/mistic/mapler

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### Bin quality

The higher the completeness and the lower the contamination, the higher the quality.

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<figure><img src="image_10.png" /><figcaption>Overview of the Mapler pipeline</figcaption></figure>

### Alignment ratios

### Unaligned reads analysis

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From the reads on contigs alignment :

* Aligned reads ratio : Aligned reads count / Total reads count

* Aligned bases ratio : Aligned bases count / Total reads length

Combined with bin quality, estimate how much diversity is captured at each level of quality.

Difference between aligned reads and bases ratio indicate partially aligned reads.

Mapler estimate divergence between aligned reads (participated in the assembly) and unaligned reads using :

* FastQC : read length, read quality

* Kraken 2 : taxonomic assignment

* KAT [3] : read abundance

<figure><img src="image_12.png" /><figcaption>Taxonomic assignment in unaligned reads of a metaMDBG rhizosphere assembly</figcaption></figure>

<caption>Abundance distribution in a metaMDBG rhizosphere assembly</caption>

## Application

### Comparing assembly methods in taxonomically rich ecosystems

In highly taxonomically-rich ecosystems such as soil, most of the diversity is uncaptured :

* Several taxa are not assembled

* Most low abundance species are not assembled

* Most of what is assembled is only partially assembled

Still, some methods fare better than others, and metaMDBG currently capture a higher proportion of the diversity at all levels of quality than competing assemblers.

Mapler is also used in the elaboration of two upcoming papers, in link with the MISTIC project of the PEPR : an application note presenting the pipeline itself and a paper on the comparison of short and long reads in soil.

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## Conclusion

Mapler is an easy-to-use evaluation pipeline that can be used to compare samples and assembly methods in taxonomically-rich ecosystems, by aggregating state-of-the-art tools and exploiting the alignment of reads on contigs.

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PROGRAMME
DE RECHERCHE

AGROÉCOLOGIE
ET NUMÉRIQUE

MISTIC

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[1] Hoysted G. et al., 2018, Curr. Op. in Pl. Bio

[2] Fierer N., 2017, Nat Rev Microbiol

[3] Mapleson D. et al., 2016, Bioinformatics