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A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE. Coil D, et al. Among authors: darling ae. Bioinformatics. 2015 Feb 15;31(4):587-9. doi: 10.1093/bioinformatics/btu661. Epub 2014 Oct 22. Bioinformatics. 2015. PMID: 25338718
Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt CONTACT: aaron.darling@uts.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt CONTACT: …
GRIL: genome rearrangement and inversion locator.
Darling AE, Mau B, Blattner FR, Perna NT. Darling AE, et al. Bioinformatics. 2004 Jan 1;20(1):122-4. doi: 10.1093/bioinformatics/btg378. Bioinformatics. 2004. PMID: 14693819
Seevolution: visualizing chromosome evolution.
Esteban-Marcos A, Darling AE, Ragan MA. Esteban-Marcos A, et al. Among authors: darling ae. Bioinformatics. 2009 Apr 1;25(7):960-1. doi: 10.1093/bioinformatics/btp096. Epub 2009 Feb 20. Bioinformatics. 2009. PMID: 19233896 Free PMC article.
Reordering contigs of draft genomes using the Mauve aligner.
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. Rissman AI, et al. Among authors: darling ae. Bioinformatics. 2009 Aug 15;25(16):2071-3. doi: 10.1093/bioinformatics/btp356. Epub 2009 Jun 10. Bioinformatics. 2009. PMID: 19515959 Free PMC article.
Metagenomic sequencing of an in vitro-simulated microbial community.
Morgan JL, Darling AE, Eisen JA. Morgan JL, et al. Among authors: darling ae. PLoS One. 2010 Apr 16;5(4):e10209. doi: 10.1371/journal.pone.0010209. PLoS One. 2010. PMID: 20419134 Free PMC article.
Mauve assembly metrics.
Darling AE, Tritt A, Eisen JA, Facciotti MT. Darling AE, et al. Bioinformatics. 2011 Oct 1;27(19):2756-7. doi: 10.1093/bioinformatics/btr451. Epub 2011 Aug 2. Bioinformatics. 2011. PMID: 21810901 Free PMC article.
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Earl D, et al. Among authors: darling a. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. Genome Res. 2011. PMID: 21926179 Free PMC article.
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.
Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Lynch EA, et al. Among authors: darling a. PLoS One. 2012;7(7):e41389. doi: 10.1371/journal.pone.0041389. Epub 2012 Jul 24. PLoS One. 2012. PMID: 22848480 Free PMC article.
An integrated pipeline for de novo assembly of microbial genomes.
Tritt A, Eisen JA, Facciotti MT, Darling AE. Tritt A, et al. Among authors: darling ae. PLoS One. 2012;7(9):e42304. doi: 10.1371/journal.pone.0042304. Epub 2012 Sep 13. PLoS One. 2012. PMID: 23028432 Free PMC article.
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