Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads (PLoS ONE (2017) 12:5 (e0176469) DOI: 10.1371/journal.pone.0176469);MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

PLoS ONE

Volumn 12, Issue 5, 2017, Pages

  Petersen, Thomas Nordahl ^a   Lukjancenko, Oksana ^a   Thomsen, Martin Christen Frølund ^a   Sperotto, Maria Maddalena ^a   Lund, Ole ^a   Aarestrup, Frank Møller ^a   Sicheritz Ponten, Thomas ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; DATA ANALYSIS; DATA BASE; GENUS; METAGENOMICS; NEXT GENERATION SEQUENCING; POPULATION ABUNDANCE; RELIABILITY; SPECIES IDENTIFICATION; TAXONOMY; WEB BROWSER; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS;

EID: 85018755906     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0179778     Document Type: Erratum

References (18)

1. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response tothaw. Nature. 2011. pp. 368-371
2. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bnlum J, Kimbrel J, et al. Metagenomics reveals sediment microbial community response toDeepwater Horizon oil spill. ISME J. 2014; 8: 1464-75. https://doi.org/10.1038/ismej.2013.254 PMID: 24451203
3. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, PicenoYM, Singh N, et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 2010; 330: 204-208. https://doi.org/10.1126/ science.1195979 PMID: 20736401
4. Hauptmann AL, Stibal M, Bnlum J, Sicheritz-Ponten T, Brunak S, Bowman JS, et al. Bacterial diversity in snow on North Pole ice floes. Extremophiles. 2014
5. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011; 473: 174-180. https://doi.org/10.1038/nature09944 PMID: 21508958
6. Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014; 32: 822-828. https://doi.org/10.1038/nbt.2939 PMID: 24997787
7. Altschul SF, Madden TL, Scha ffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Research. 1997. pp. 3389-3402. PMID: 9254694
8. Peabody MA, Van Rossum T, LoR, Brinkman FSL. Evaluation of shotgun metagenomics sequence classification methods using in silicoand in vitrosimulated communities. BMC Bioinformatics. BMC Bioinformatics; 2015; 16: 363
9. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014; 15: R46. https://doi.org/10.1186/gb-2014-15-3-r46 PMID: 24580807
10. Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 2011; 39
11. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007; 17: 377-386. https://doi.org/10.1101/gr.5969107 PMID: 17255551
12. Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011; 21: 1552-1560. https://doi.org/10.1101/gr.120618. 111 PMID: 21690186
13. ZhaoY, Tang H, Ye Y. RAPSearch2: A fast and memory-efficient protein similarity search tool for nextgeneration sequencing data. Bioinformatics. 2012; 28: 125-126. https://doi.org/10.1093/bioinformatics/ btr595 PMID: 22039206
14. Larsen M V., CosentinoS, LukjancenkoO, Saputra D, Rasmussen S, Hasman H, et al. Benchmarking of methods for genomic taxonomy. J Clin Microbiol. 2014; 52: 1529-1539. https://doi.org/10.1128/JCM. 02981-13 PMID: 24574292
15. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26: 589-595. https://doi.org/10.1093/bioinformatics/btp698 PMID: 20080505
16. Meyer F, Paarmann D, DSouza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9: 386. https://doi.org/10.1186/1471-2105-9-386 PMID: 18803844
17. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17: 10
18. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25: 2078-2079. https://doi.org/10.1093/bioinformatics/btp352 PMID: 19505943