Cbcb:Pop-Lab:Papers: Difference between revisions
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# McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.] | # McHardy AC, Rigoutsos I. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4PYJF84-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000049425&_version=1&_urlVersion=0&_userid=961305&md5=316fa2bf95026562f743d2b70641e793 What's in the mix: phylogenetic classification of metagenome sequence samples.] | ||
# Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities] | # Kevin Chen, Lior Pachter [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010024;jsessionid=9A83C77149D62FDAD8ACBBA40B0FE07E Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities] | ||
# Foerstner KU, von Mering C, Bork P. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16524840 Comparative analysis of environmental sequences: potential and challenges] | |||
== Pioneering papers == | == Pioneering papers == | ||
Revision as of 17:45, 19 February 2009
Metagenomics Reviews
- V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
- Clarridge J.E. 16S sequencing and clinical microbiology review
- C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
- J. Eisen. Light metagenomics review for GOS expedition.
- Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene
- Warnecke F, Hugenholtz P. Building on basic metagenomics with complementary technologies
- Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data.
- McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples.
- Kevin Chen, Lior Pachter Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
- Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges
Pioneering papers
- G Muyzer, E C de Waal and A G Uitterlinden PCR amplifying 16S rRNA genes and DGGE
- D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
16S sequence analysis
- Classification.
- RDP classifier
- BLAST searches
- Multilocus classification
- Sogin-like database search methods
- Sanger vs. 454
- Alignment.
- ClustalW
- NAST
- MUSCLE
- Pairwise
- Masking approaches (LaneMask)
- Distance corrections.
- Jukes-Cantor
- Kimura-2
- Felsenstein84
- Olsen
- Clustering.
- DOTUR
- VI-cut
- OTU picker (unpublished)
- Database versions (Sogin papers)
- Community comparison.
- Diversity estimators
- Rarefaction curves
- DOTUR
- EstimateS
- SONs
- TreeClimber
- S-libshuff
- UniFrac
- MEGAN
- Xipe - single sample comparisons
- Metastats