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Improving recovery of member genomes from enrichment reactor microbial communities using MinION–based long read metagenomics

https://doi.org/10.1101/465328
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants
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Basic Local Alignment Search Tool
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STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT
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Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization
inferredcites →https://doi.org/10.1038/ismej.2017.126openalex-snapshot
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
inferredcites →https://doi.org/10.1038/nbt.3880openalex-snapshot
Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding
inferredcites →https://doi.org/10.1038/nbt.3893openalex-snapshot
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
inferredcites →https://doi.org/10.1038/nbt0718-660aopenalex-snapshot
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
inferredcites →https://doi.org/10.1038/ncomms14306openalex-snapshot
MetaSort untangles metagenome assembly by reducing microbial community complexity
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/s41467-018-03317-6openalex-snapshot
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
inferredcites →https://doi.org/10.1038/s41564-018-0176-9openalex-snapshot
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
inferredcites →https://doi.org/10.1038/s41598-018-23053-7openalex-snapshot
Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing
inferredcites →https://doi.org/10.1038/sdata.2016.81openalex-snapshot
Next generation sequencing data of a defined microbial mock community
inferredcites →https://doi.org/10.1038/srep25373openalex-snapshot
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts252openalex-snapshot
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btx370openalex-snapshot
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/gigascience/gix007openalex-snapshot
MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
inferredcites →https://doi.org/10.1093/nar/gkm864openalex-snapshot
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
inferredcites →https://doi.org/10.1093/nar/gkq275openalex-snapshot
Ab initio gene identification in metagenomic sequences
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkx348openalex-snapshot
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation
inferredcites →https://doi.org/10.1093/nar/gkz148openalex-snapshot
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes
inferredcites →https://doi.org/10.1099/mgen.0.000132openalex-snapshot
Completing bacterial genome assemblies with multiplex MinION sequencing
inferredcites →https://doi.org/10.1101/124131openalex-snapshot
SEARCH_16S: A new algorithm for identifying 16S ribosomal RNA genes in contigs and chromosomes
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1128/genomea.00111-18openalex-snapshot
Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment
inferredcites →https://doi.org/10.1186/s12859-016-1378-xopenalex-snapshot
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
inferredcites →https://doi.org/10.1186/s13059-017-1309-9openalex-snapshot
DESMAN: a new tool for de novo extraction of strains from metagenomes
inferredcites →https://doi.org/10.1186/s13062-018-0208-7openalex-snapshot
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
inferredcites →https://doi.org/10.1186/s40793-017-0224-8openalex-snapshot
Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
inferredcites →https://doi.org/10.1534/g3.114.011825openalex-snapshot
Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
inferredcites →https://doi.org/10.3389/fmicb.2018.00193openalex-snapshot
Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland
inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.zool.2019.125695openalex-snapshot
Molecular techniques and their limitations shape our view of the holobiont
inferred← citeshttps://doi.org/10.1101/2020.03.12.974238openalex-snapshot
Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing
inferred← citeshttps://doi.org/10.1101/585067openalex-snapshot
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
inferred← citeshttps://doi.org/10.35825/2587-5728-2023-7-4-366-383openalex-snapshot
Modern Bioinformatics Solutions Used for Genetic Data Analysis
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