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References from A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Local targets link to admitted publications; unresolved targets remain external evidence.
The Human Intestinal Microbiome in Health and Disease
10.1056/nejmra1600266 · 2016 · External reference
10.1111/jpc.14939
10.1111/jpc.14939 · External reference
A metagenomics approach to investigate microbiome sociobiology
10.1073/pnas.2100934118 · 2021 · External reference
As the Microbiome Moves on toward Mechanism
10.1016/j.molcel.2020.05.006 · 2020 · External reference
Shift in the paradigm towards next-generation microbiology
10.1093/femsle/fnz159 · 2019 · External reference
10.1093/bib/bbz155
10.1093/bib/bbz155 · External reference
Microbiome definition re-visited: old concepts and new challenges
2020 · External reference
Culture of previously uncultured members of the human gut microbiota by culturomics
2016 · External reference
10.1038/nature17645
10.1038/nature17645 · External reference
10.1038/s41586-019-1058-x
10.1038/s41586-019-1058-x · External reference
10.1038/s41591-019-0405-7
10.1038/s41591-019-0405-7 · External reference
10.1016/j.chom.2019.07.004
10.1016/j.chom.2019.07.004 · External reference
Challenges in benchmarking metagenomic profilers
10.1038/s41592-021-01141-3 · 2021 · External reference
10.1038/nmeth.2693
10.1038/nmeth.2693 · External reference
10.1101/gr.201863.115
10.1101/gr.201863.115 · External reference
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
2016 · External reference
10.1093/bioinformatics/btz253
10.1093/bioinformatics/btz253 · External reference
BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage
2018 · External reference
10.1016/j.cell.2019.01.001
10.1016/j.cell.2019.01.001 · External reference
10.1038/s41587-020-0603-3
10.1038/s41587-020-0603-3 · External reference
10.1038/s41586-019-0965-1
10.1038/s41586-019-0965-1 · External reference
Quality control of next-generation sequencing data without a reference
10.3389/fgene.2014.00111 · 2014 · External reference
Opportunities and challenges in long-read sequencing data analysis
10.1186/s13059-020-1935-5 · 2020 · External reference
10.1093/bioinformatics/bty560
10.1093/bioinformatics/bty560 · External reference
10.1093/bioinformatics/btu170
10.1093/bioinformatics/btu170 · External reference
SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
10.1093/gigascience/gix120 · 2018 · External reference
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
10.1186/s12859-020-03751-8 · 2020 · External reference
10.1093/bioinformatics/btu392
10.1093/bioinformatics/btu392 · External reference
10.1093/bioinformatics/bty149
10.1093/bioinformatics/bty149 · External reference
MinIONQC: Fast and simple quality control for MinION sequencing data
10.1093/bioinformatics/bty654 · 2019 · External reference
A quality control tool for third generation sequencing long read data
10.1534/g3.119.400864 · 2020 · External reference
10.1101/gr.245126.118
10.1101/gr.245126.118 · External reference
10.1101/gr.260380.119
10.1101/gr.260380.119 · External reference
10.1038/nbt.3416
10.1038/nbt.3416 · External reference
Omega: an overlap-graph de novo assembler for metagenomics
10.1093/bioinformatics/btu395 · 2014 · External reference
10.1093/nar/gks678
10.1093/nar/gks678 · External reference
10.1101/gr.074492.107
10.1101/gr.074492.107 · External reference
An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
10.1093/dnares/dsu041 · 2015 · External reference
MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly
2021 · External reference
10.1093/bioinformatics/bts174
10.1093/bioinformatics/bts174 · External reference
10.1093/bioinformatics/btv033
10.1093/bioinformatics/btv033 · External reference
10.1016/j.ymeth.2016.02.020
10.1016/j.ymeth.2016.02.020 · External reference
10.1101/gr.213959.116
10.1101/gr.213959.116 · External reference
10.1089/cmb.2012.0021
10.1089/cmb.2012.0021 · External reference
Ray Meta: scalable de novo metagenome assembly and profiling
10.1186/gb-2012-13-12-r122 · 2012 · External reference
10.1038/nbt.4266
10.1038/nbt.4266 · External reference
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs
10.1093/bioinformatics/btz349 · 2019 · External reference
10.1101/gr.097261.109
10.1101/gr.097261.109 · External reference
10.1126/science.287.5461.2196
10.1126/science.287.5461.2196 · External reference
Minimus: a fast, lightweight genome assembler
2007 · External reference
10.1101/gr.215087.116
10.1101/gr.215087.116 · External reference
Efficient assembly of nanopore reads via highly accurate and intact error correction
2021 · External reference
10.1038/s41592-019-0669-3
10.1038/s41592-019-0669-3 · External reference
10.1038/s41592-020-00971-x
10.1038/s41592-020-00971-x · External reference
10.1038/s41587-019-0072-8
10.1038/s41587-019-0072-8 · External reference
DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
2016 · External reference
10.1038/s41587-019-0191-2
10.1038/s41587-019-0191-2 · External reference
Resolving bacterial genome assemblies from short and long sequencing reads
10.1371/journal.pcbi.1005595 · 2017 · External reference
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
2020 · External reference
10.1093/bioinformatics/btv697
10.1093/bioinformatics/btv697 · External reference
10.1093/bioinformatics/btv231
10.1093/bioinformatics/btv231 · External reference
REAPR: a universal tool for genome assembly evaluation
10.1186/gb-2013-14-5-r47 · 2013 · External reference
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
10.1093/bib/bbx098 · 2019 · External reference
10.1093/bioinformatics/btaa124
10.1093/bioinformatics/btaa124 · External reference
10.7717/peerj.603
10.7717/peerj.603 · External reference
10.1093/bioinformatics/btv638
10.1093/bioinformatics/btv638 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
10.7717/peerj.7359
10.7717/peerj.7359 · External reference
GraphBin: refined binning of metagenomic contigs using assembly graphs
10.1093/bioinformatics/btaa180 · 2020 · External reference
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
10.1186/s12859-021-04284-4 · 2021 · External reference
10.1038/s41587-020-00777-4
10.1038/s41587-020-00777-4 · External reference
Auto-Encoding Variational Bayes. 2nd Int Conf Learn Represent ICLR 2014 -
2013 · External reference
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes
10.1093/molbev/msz237 · 2020 · External reference
MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis
10.1186/s40168-018-0541-1 · 2018 · External reference
10.1038/s41564-018-0171-1
10.1038/s41564-018-0171-1 · External reference
Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions
2017 · External reference
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
10.1186/s13059-019-1643-1 · 2019 · External reference
10.1016/j.csbj.2021.06.052
10.1016/j.csbj.2021.06.052 · External reference
Binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
2021 · External reference
Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression
2021 · External reference
10.1101/gr.186072.114
10.1101/gr.186072.114 · External reference
10.1038/nbt.3893
10.1038/nbt.3893 · External reference
10.1038/s41564-017-0012-7
10.1038/s41564-017-0012-7 · External reference
10.1093/nar/gkq275
10.1093/nar/gkq275 · External reference
10.1093/nar/gkr1067
10.1093/nar/gkr1067 · External reference
10.1093/nar/gkq747
10.1093/nar/gkq747 · External reference
Prodigal: prokaryotic gene recognition and translation initiation site identification
10.1186/1471-2105-11-119 · 2010 · External reference
10.1093/nar/gkl723
10.1093/nar/gkl723 · External reference
detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
10.1093/dnares/dsn027 · 2008 · External reference
10.1155/2017/4740354
10.1155/2017/4740354 · External reference
Convolutional Neural Networks for Metagenomics Gene Prediction
10.1007/s12539-018-0313-4 · 2019 · External reference
A universal protein model for prokaryotic gene prediction
10.1371/journal.pcbi.1008727 · 2021 · External reference
10.1093/nar/gkt282
10.1093/nar/gkt282 · External reference
10.1093/molbev/msx148
10.1093/molbev/msx148 · External reference
10.1016/j.jmb.2015.11.006
10.1016/j.jmb.2015.11.006 · External reference
10.1007/978-1-4939-3369-3_13
10.1007/978-1-4939-3369-3_13 · External reference
10.1093/nar/gky350
10.1093/nar/gky350 · External reference
10.1093/nar/gky1085
10.1093/nar/gky1085 · External reference
10.1007/978-1-4939-7015-5_2
10.1007/978-1-4939-7015-5_2 · External reference
new perspectives on genomes, pathways, diseases and drugs
10.1093/nar/gkw1092 · 2017 · External reference
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
10.1186/1471-2105-13-141 · 2012 · External reference
SANSparallel: interactive homology search against Uniprot
10.1093/nar/gkv317 · 2015 · External reference
20 years and still GOing strong
10.1093/nar/gky1055 · 2019 · External reference
10.1093/nar/29.1.37
10.1093/nar/29.1.37 · External reference
10.1093/nar/gkp885
10.1093/nar/gkp885 · External reference
PRINTS–a protein motif fingerprint database
10.1093/protein/7.7.841 · 1994 · External reference
10.1093/nar/gki442
10.1093/nar/gki442 · External reference
Advantages of combined transmembrane topology and signal peptide prediction–the Phobius web server
10.1093/nar/gkm256 · 2007 · External reference
10.1073/pnas.0702636104
10.1073/pnas.0702636104 · External reference
GeConT: gene context analysis
10.1093/bioinformatics/bth216 · 2004 · External reference
10.1093/nar/gkaa1018
10.1093/nar/gkaa1018 · External reference
FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information
10.1093/bioinformatics/btz957 · 2020 · External reference
10.1093/nar/gkt1223
10.1093/nar/gkt1223 · External reference
Predicting Functional Associations using Flanking Genes (FlaGs)
2018 · External reference
10.1093/bioinformatics/btz848
10.1093/bioinformatics/btz848 · External reference
10.1371/journal.pcbi.1002195
10.1371/journal.pcbi.1002195 · External reference
10.1038/nbt.4229
10.1038/nbt.4229 · External reference
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
10.1186/1471-2105-11-538 · 2010 · External reference
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
2018 · External reference
10.1093/molbev/msp077
10.1093/molbev/msp077 · External reference
10.1038/s41467-020-16366-7
10.1038/s41467-020-16366-7 · External reference
10.1093/nar/gky467
10.1093/nar/gky467 · External reference
Fast and sensitive taxonomic classification for metagenomics with Kaiju
10.1038/ncomms11257 · 2016 · External reference
Unresolved reference
1994 · External reference
Opportunistic data structures with applications
10.1109/sfcs.2000.892127 · 2000 · External reference
ultrafast metagenomic sequence classification using exact alignments
2014 · External reference
Improved metagenomic analysis with Kraken 2
2019 · External reference
Bracken: estimating species abundance in metagenomics
10.7717/peerj-cs.104 · 2017 · External reference
fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
10.1186/s12864-015-1419-2 · 2015 · External reference
10.1093/nar/gkw1248
10.1093/nar/gkw1248 · External reference
10.7554/elife.65088
10.7554/elife.65088 · External reference
10.1038/nbt.3319
10.1038/nbt.3319 · External reference
10.1016/j.chom.2018.01.003
10.1016/j.chom.2018.01.003 · External reference
Strain profiling and epidemiology of bacterial species from metagenomic sequencing
2017 · External reference
A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
10.3389/fmicb.2018.03349 · 2019 · External reference
10.1371/journal.pone.0177459
10.1371/journal.pone.0177459 · External reference
10.1371/journal.pone.0169662
10.1371/journal.pone.0169662 · External reference
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
2020 · External reference
10.1038/nmeth.4458
10.1038/nmeth.4458 · External reference
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
2020 · External reference
Critical Assessment of Metagenome Interpretation - the second round of challenges
2021 · External reference
No one tool to rule them all: Prokaryotic gene prediction tool performance is highly dependent on the organism of study
2021 · External reference
10.1016/j.cell.2019.07.010
10.1016/j.cell.2019.07.010 · External reference
10.1101/gr.258640.119
10.1101/gr.258640.119 · External reference
GUNC: detection of chimerism and contamination in prokaryotic genomes
10.1186/s13059-021-02393-0 · 2021 · External reference
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
10.1038/s41587-020-0422-6 · 2020 · External reference
Real-time selective sequencing using nanopore technology
10.1038/nmeth.3930 · 2016 · External reference
10.1038/s41587-020-0731-9
10.1038/s41587-020-0731-9 · External reference
Advances and Challenges in Metatranscriptomic Analysis
10.3389/fgene.2019.00904 · 2019 · External reference
10.1089/cmb.2014.0139
10.1089/cmb.2014.0139 · External reference
10.1093/bioinformatics/btv510
10.1093/bioinformatics/btv510 · External reference
Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms
2021 · External reference
Unresolved reference
External reference
10.1016/j.cell.2019.07.016
10.1016/j.cell.2019.07.016 · External reference
10.1038/nrg3520
10.1038/nrg3520 · External reference
10.1093/nar/gkab776
10.1093/nar/gkab776 · External reference
STRONG: metagenomics strain resolution on assembly graphs
10.1186/s13059-021-02419-7 · 2021 · External reference
Genome-resolved metagenomics using environmental and clinical samples
2021 · External reference