title: Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.
abstract: While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.
authors.affiliation: Computational and Mathematical Biology, Genome Institute of Singapore 127726, Singapore. niranjan@umiacs.umd.edu
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
authors.forename: Christopher
authors.initials: C
authors.lastname: Cook
authors.forename: Mariapia
authors.initials: M
authors.lastname: Di Bonaventura
authors.forename: Hong
authors.initials: H
authors.lastname: Ge
authors.forename: Allen
authors.initials: A
authors.lastname: Richards
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Bishop-Lilly
authors.forename: Robert
authors.initials: R
authors.lastname: DeSalle
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Read
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
mesh_terms: D020563:Gammaproteobacteria / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D012283:Rickettsia prowazekii / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D015007:Yersinia / Q000235:genetics*
references.citation: Genome Res. 1995 Aug;5(1):1-4
references.pmid: 8717049
references.citation: Bioinformatics. 2008 Dec 15;24(24):2818-24
references.pmid: 18952627
references.citation: Nature. 1998 Nov 12;396(6707):133-40
references.pmid: 9823893
references.citation: J Bacteriol. 2002 Dec;184(23):6403-5; discusion 6405
references.pmid: 12426324
references.citation: BMC Genomics. 2007 Sep 14;8:321
references.pmid: 17868451
references.citation: J Bacteriol. 2009 Jul;191(14):4693-4
references.pmid: 19447908
references.citation: Genomics. 1999 Dec 15;62(3):500-7
references.pmid: 10644449
references.citation: J Bacteriol. 2002 Dec;184(23):6406-9; discussion 6409
references.pmid: 12426325
references.citation: J Comput Biol. 2009 Jul;16(7):897-908
references.pmid: 19580519
references.citation: Science. 2000 Mar 24;287(5461):2196-204
references.pmid: 10731133
references.citation: Pac Symp Biocomput. 2002;:199-210
references.pmid: 11928476
references.citation: PLoS Comput Biol. 2008 Sep 26;4(9):e1000186
references.pmid: 18818729
references.citation: Bioinformatics. 2007 Nov 1;23(21):2942-4
references.pmid: 17893086
references.citation: Genome Res. 2008 Feb;18(2):324-30
references.pmid: 18083777
references.citation: Bioinformatics. 2007 Jul 1;23(13):1573-9
references.pmid: 17463020
references.citation: Bioinformatics. 2008 May 15;24(10):1229-35
references.pmid: 18356192
references.citation: Nat Biotechnol. 2000 May;18(5):493-4
references.pmid: 10802612
references.citation: Genome Biol. 2010 Jan 04;11(1):R1
references.pmid: 20047673
references.citation: BMC Bioinformatics. 2007 Feb 26;8:64
references.pmid: 17324286
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2673-8
references.pmid: 17296933
references.citation: Nucleic Acids Res. 2008 Jun;36(10):3455-62
references.pmid: 18445633