Reference list

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