title: Metagenome-assembled genome: ERP118353_co1_131
organism: uncultured Pseudomonadales bacterium
description: This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs ERR3654040,ERR3654041 of study ERP118353.
attributes.tag: ENA first public
attributes.value: 2024-12-11
attributes.tag: INSDC center name
attributes.value: CMR
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: ERP118353_co1_131
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaSPAdes;3.15.4;default
attributes.tag: binning parameters
attributes.value: coverage and kmer
attributes.tag: binning software
attributes.value: MetaBAT;2.15;default
attributes.tag: broad-scale environmental context
attributes.value: aquatic
attributes.tag: collection date
attributes.value: 2018-12-11
attributes.tag: completeness score
attributes.value: 75.38
attributes.tag: completeness software
attributes.value: CheckM2;1.0.2;default
attributes.tag: contamination score
attributes.value: 0.36
attributes.tag: environmental medium
attributes.value: aquatic
attributes.tag: geographic location (country and/or sea)
attributes.value: not provided
attributes.tag: geographic location (latitude)
attributes.value: not provided
attributes.tag: geographic location (longitude)
attributes.value: not provided
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: groundwater metagenome
attributes.tag: local environmental context
attributes.value: groundwater biome
attributes.tag: metagenomic source
attributes.value: groundwater metagenome
attributes.tag: project name
attributes.value: Assembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments that are dominated by uncultured and/or under-studied groups. This study aimed to investigate the impact of incorporating long-read data into the process of reconstructing metagenome-assembled genomes (MAGs) from a complex groundwater aquifer. We generated shotgun metagenomes with traditional Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups. Groundwater was collected from the Hainich Critical Zone Exploratory, a near-surface aquifer transect that is established in NW Thuringia, Germany. This data set is part of the DFG-funded CRC AquaDiva (https://www.aquadiva.uni-jena.de/) of the Friedrich Schiller University Jena.
attributes.tag: sample derived from
attributes.value: SAMEA6167471,SAMEA6167472
attributes.tag: sample name
attributes.value: ERP118353_co1_131
attributes.tag: scientific_name
attributes.value: uncultured Pseudomonadales bacterium
attributes.tag: sequencing method
attributes.value: Illumina MiSeq
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach