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Reference list
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General references

   NGS wikibook: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)
   NGS field guide http://www.molecularecologist.com/next-gen-fieldguide-2013

Looking at 16S and whole transcriptome:

   Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T, Schleper C (2012)
   Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and
   function of its microbial community. Environmental Microbiology 14(5):
   1308-1324. doi: 10.1111/j.1462-2920.2012.02714.x.

Assembling symbiont communities with digital normalization:

   K Goffredi S, Yi H, Zhang Q, Klann JE, Struve IA, Vrijenhoek RC, Brown CT.
   Genomic versatility and functional variation between two dominant heterotrophic
   symbionts of deep-sea Osedax worms. ISME J. 2013 Nov 14. doi: 10.1038/ismej.2013.201.

Assembling messy eukaryotic genomes with digital normalization:

   Schwarz EM, Korhonen PK, Campbell BE, Young ND, Jex AR, Jabbar A, Hall RS,
   Mondal A, Howe AC, Pell J, Hofmann A, Boag PR, Zhu XQ, Gregory TR, Loukas A,
   Williams BA, Antoshechkin I, Brown CT, Sternberg PW, Gasser RB. The genome and
   developmental transcriptome of the strongylid nematode Haemonchus contortus.
   Genome Biol. 2013 Aug 28;14(8):R89.

Assembling soil with partitioning and digital normalization:

   Assembling large, complex environmental genomes.  Howe et al.,
   arXiv (http://arxiv.org/abs/1212.2832).

Variant calling (including structural variants):

   Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G. De novo assembly and
   genotyping of variants using colored de Bruijn graphs. Nat Genet. 2012 Jan
   8;44(2):226-32. doi: 10.1038/ng.1028. PubMed PMID: 22231483; PubMed Central
   PMCID: PMC3272472.

   Iqbal Z, Turner I, McVean G. High-throughput microbial population genomics
   using the Cortex variation assembler. Bioinformatics. 2013 Jan 15;29(2):275-6.
   doi: 10.1093/bioinformatics/bts673. Epub 2012 Nov 19. PubMed PMID: 23172865;
   PubMed Central PMCID: PMC3546798.

   Leggett RM, Ramirez-Gonzalez RH, Verweij W, Kawashima CG, Iqbal Z, Jones JD,
   Caccamo M, Maclean D. Identifying and classifying trait linked polymorphisms in
   non-reference species by walking coloured de bruijn graphs. PLoS One.
   2013;8(3):e60058. doi: 10.1371/journal.pone.0060058. Epub 2013 Mar 25. PubMed
   PMID: 23536903; PubMed Central PMCID: PMC3607606.




Using chromatin interactions data (Hi-C) for scaffolding assemblies:

   Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2727.html

   High-throughput genome scaffolding from in vivo DNA interaction frequency http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2768.html


Trimming/filtering references:

  On the optimal trimming of high-throughput mRNA sequence data. MacManes.
  http://biorxiv.org/content/early/2013/11/14/000422
  
Q/A Resources

  http://www.biostars.org/
  
  http://seqanswers.com/

Binning: Genomes from Metangenomes

  CONCOCT: Clustering cONtigs on COverage and ComposiTion
  http://arxiv.org/abs/1312.4038

  Multi-metagenome scripts
  http://madsalbertsen.github.io/multi-metagenome/

  Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
  http://www.nature.com/nbt/journal/v31/n6/full/nbt.2579.html
  Also see presentation slides here:
  http://www.slideshare.net/MadsAlbertsen/20131202-mads-albertsen-extracting-genomes-from-metagenomes

  The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
  http://elife.elifesciences.org/content/2/e01102

  Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
  http://genome.cshlp.org/content/23/1/111.full