MGAviewer: A desktop visualization tool for analysis of metagenomics alignment data

Bioinformatics

Volumn 29, Issue 1, 2013, Pages 122-123

  Zhu, Zhengwei ^a   Niu, Beifang ^a   Chen, Jing ^a   Wu, Sitao ^a   Sun, Shulei ^a   Li, Weizhong ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; GENOME; HUMAN; INTERNET; METAGENOMICS; METHODOLOGY; SEQUENCE ALIGNMENT;

COMPUTER GRAPHICS; GENOME; HUMANS; INTERNET; METAGENOMICS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84871799128     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts567     Document Type: Article

References (16)

1. Abeel, T. et al. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res., 40, e12.
2. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
3. Bao, H. et al. (2009) MapView: visualization of short reads alignment on a desktop computer. Bioinformatics, 25, 1554-1555.
4. Dreszer, T.R. et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res., 40, D918-D923.
5. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
6. Manske, H.M. and Kwiatkowski, D.P. (2009) LookSeq: a browser-based viewer for deep sequencing data. Genome Res., 19, 2125-2132.
7. Mardis, E.R. (2011) A decade's perspective on DNA sequencing technology. Nature, 470, 198-203.
8. Milne, I. et al. (2010) Tablet-next generation sequence assembly visualization. Bioinformatics, 26, 401-402.
9. Nicol, J.W. et al. (2009) The integrated genome browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics, 25, 2730-2731.
10. Niu, B. et al. (2011) FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Bioinformatics, 27, 1704-1705.
11. Popendorf, K. and Sakakibara, Y. (2012) SAMSCOPE: an openGL-based real-time interactive scale-free SAM viewer. Bioinformatics, 28, 1276-1277.
12. Qin, J. et al. (2010) A human gut microbial gene catalogue established by metage-nomic sequencing. Nature, 464, 59-65.
13. Robinson, J.T. et al. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26.
14. Rusch, D.B. et al. (2007) The sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol., 5, e77.
15. Skinner, M.E. et al. (2009) JBrowse: a next-generation genome browser. Genome Res., 19, 1630-1638.
16. Sun, S. et al. (2011) Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res., 39, D546-D551.