Cbcb:Pop-Lab:Papers

Metagenomics Reviews

1. V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
2. Clarridge J.E. 16S sequencing and clinical microbiology review
3. C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
4. J. Eisen. Light metagenomics review for GOS expedition.
5. Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene
6. Warnecke F, Hugenholtz P. Building on basic metagenomics with complementary technologies
7. Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data.

Pioneering papers

1. G Muyzer, E C de Waal and A G Uitterlinden PCR amplifying 16S rRNA genes and DGGE
2. 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  • OTU picker (unpublished)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