The impact of Docker containers on the performance of genomic pipelines

PeerJ

Volumn 2015, Issue 9, 2015, Pages

  Di Tommaso, Paolo ^a,b   Palumbo, Emilio ^a,b   Chatzou, Maria ^a,b   Prieto, Pablo ^a,b   Heuer, Michael L ^c   Notredame, Cedric ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c NATIONAL MARROW DONOR PROGRAM   (United States)

Author keywords

Bioinformatics; Docker; Pipelines; Virtualisation; Workflow

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DRB1 ANTIGEN; KILLER CELL IMMUNOGLOBULIN LIKE RECEPTOR;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DNA PACKAGING; GENE MAPPING; GENOMICS; HUMAN; MOLECULAR DOCKING; NEXT GENERATION SEQUENCING; NONHUMAN; PIPELINE; RNA SEQUENCE; SEQUENCE ANALYSIS; WORKFLOW;

EID: 84944903287     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1273     Document Type: Article

References (19)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3):403-410 DOI 10.1016/S0022-2836(05)80360-2.
2. Boettiger C. 2015. An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review, Special Issue on Repeatability and Sharing of Experimental Artifacts 49(1):71-79 DOI 10.1145/2723872.2723882.
3. Di Tommaso P, Chatzou M, Baraja P, Notredame C. 2014. Nextflow: a novel tool for highly scalable computational pipelines. Available at http://dx.doi.org/10.6084/m9.figshare.1254958.
4. ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74 DOI 10.1038/nature11247.
5. Felter W, Ferreira A, Rajamony R, Rubio J. 2014. An updated performance comparison of virtual machines and linux contain. IBM Research Available at http://ibm.co/V55Otq(accessed 1 June 2015).
6. Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne PE, Gil Y. 2013. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS ONE 8(11):e80278 DOI 10.1371/journal.pone.0080278.
7. Gent IP. 2013. The recomputation manifesto. ArXiv preprint. arXiv:1304.3674.
8. Gerlach W, Tang W, Keegan K, Harrison T, Wilke A, Bischof J, D'Souza M, Devoid S, Murphy-Olson D, Desai N, Meyer F. 2014. Skyport: container-based execution environment management for multi-cloud scientific workflows. In: Proceedings of the 5th international workshop on data-intensive computing in the clouds. DataCloud'14. Piscataway: IEEE Press, 25-32.
9. Hinsen K. 2014. ActivePapers: a platform for publishing and archiving computer-aided research. F1000Research 3:289 DOI 10.12688/f1000research.5773.3.
10. Howe B. 2012. Virtual appliances, cloud computing, and reproducible research. Computing in Science Engineering 14(4):36-41 DOI 10.1109/MCSE.2012.62.
11. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14(4):R36 DOI 10.1186/gb-2013-14-4-r36.
12. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9(4):357-359 DOI 10.1038/nmeth.1923.
13. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760 DOI 10.1093/bioinformatics/btp324.
14. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079 DOI 10.1093/bioinformatics/btp352.
15. Mack SJ, Milius RP, Gifford BD, Sauter J, Hofmann J, Osoegawa K, Robinson J, Groeneweg M, Turenchalk GS, Adai A, Holcomb C, Rozemuller EH, Penning MT, Heuer ML, Wang C, Salit ML, Schmidt AH, Müller C, Hague T, Fischer G, Fernandez-Via M, Hollenbach JA, Norman PJ, Maiers M. 2015. Minimum information for reporting next generation sequence genotyping (MIRING): guidelines for reporting HLA and KIR genotyping via next generation sequencing. Available at http://biorxiv.org/content/early/2015/02/16/015230(accessed 1 June 2015).
16. Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302(1):205-217 DOI 10.1006/jmbi.2000.4042.
17. Slater GSC, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31 DOI 10.1186/1471-2105-6-31.
18. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28:511-515 DOI 10.1038/nbt.1621.
19. Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23(4):500-501 DOI 10.1093/bioinformatics/btl629.