RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity

Abstract

Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample. Hence, RecruitPlotEasy should also greatly facilitate population genetics studies.RecruitPlotEasy is implemented in Python and R languages and is freely available open source software under the Artistic License 2.0 from https://github.com/KGerhardt/RecruitPlotEasy.

Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila

“…That is, when the MAG of this study was classified at least at the genus level by the GTDB-tk software, a genome of the same taxonomic genus was selected, provided it was available in the NCBI RefSeq databases (refer to Supplementary Table S4 for information about the 17 reference genomes used in this analysis). To perform metagenomic recruitment analysis with Recruiteasy ( Gerhardt et al, 2022 ) software, the mapping of sequencing reads to relevant reference genomes was performed using the bowtiew2 and samtools softwares. For example, the reference genome of Halothece sp.…”

Discovery of the Streamlined Haloarchaeon Halorutilus salinus , Comprising a New Order Widespread in Hypersaline Environments across the World

“…The abundance of strain F3-133 T in available metagenomes was assessed by read fragment recruitment plots ( 94 ). For this, the genome sequence of strain F3-133 T was searched against all metagenomic reads from each data set ( Table S2 ) using stand-alone BLASTn.…”

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

“…Cellulosimicrobium cellulans reads were excluded from all the datasets during the analysis as their presence is due to the lyticase used for yeast lysis during DNA extraction [38,39]. The reference genomes in RefSeq of the most abundant species were employed to construct recruitment plots using the RecruitPlotEasy software with the default settings [40]. The initial step of mapping the sequence reads against the reference genomes was performed with the CLC genomics workbench.…”