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In Print: Last Week's Sequencing-Related Papers of Note: Mar 26, 2013


Comparative studies of copy number variation detection methods for next-generation sequencing technologies.
Duan J, Zhang JG, Deng HW, Wang YP.
PLoS One. 2013;8(3):e59128.

A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range.
Quéméré E, Hibert F, Miquel C, Lhuillier E, et al.
PLoS One. 2013;8(3):e58971.

SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.
Sun X, Liu D, Zhang X, Li W, et al.
PLoS One. 2013;8(3):e58700.

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, et al.
Genome Res. 2013 Mar 22. [Epub ahead of print]

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle.
Zhan X, Pan S, Wang J, Dixon A, et al.
Nat Genet. 2013 Mar 24. [Epub ahead of print]

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
The International Peach Genome Initiative, Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, et al.
Nat Genet. 2013 Mar 24. [Epub ahead of print]

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.
Desjardins CA, Cerqueira GC, Goldberg JM, Hotopp JC, et al.
Nat Genet. 2013 Mar 24. [Epub ahead of print]

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-seq.
Wery M, Descrimes M, Thermes C, Gautheret D, Morillon A.
Methods. 2013 Mar 20. [Epub ahead of print]

A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model.
Ramírez C, Gregori J, Buti M, Tabernero D, et al.
Antiviral Res. 2013 Mar 19. [Epub ahead of print]

LASAGNA: a novel algorithm for transcription factor binding site alignment.
Lee C, Huang CH.
BMC Bioinformatics. 2013 Mar 24;14(1):108.

Pervasive sequence patents cover the entire human genome.
Rosenfeld J, Mason CE.
Genome Med. 2013 Mar 25;5(3):27.

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Farrer RA, Henk DA, Maclean D, Studholme DJ, Fisher MC.
Sci Rep. 2013 Mar 22;3:1512.

Genome sequences of wild and domestic bactrian camels.
Bactrian Camels Genome Sequencing and Analysis Consortium, Jirimutu, Wang Z, Ding G, Nat Commun. 2012;3:1202.

Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity.
Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D.
PLoS One. 2013;8(3):e58950.

An artificial functional family filter in homolog searching in next-generation sequencing metagenomics.
Du R, Mercante D, Fang Z.
PLoS One. 2013;8(3):e58669.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
Feng Z, Fang G, Korlach J, Clark T, et al.
PLoS Comput Biol. 2013 Mar;9(3):e1002935.

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.
Xu J, Li Y, Ma X, Ding J, et al.
Plant Mol Biol. 2013 Mar 20. [Epub ahead of print]

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data.
Skennerton CT, Imelfort M, Tyson GW.
Nucleic Acids Res. 2013 Mar 19. [Epub ahead of print]

Whole-genome haplotyping by dilution, amplification, and sequencing.
Kaper F, Swamy S, Klotzle B, Munchel S, et al.
Proc Natl Acad Sci U S A. 2013 Mar 18. [Epub ahead of print]
(See our coverage of this paper here.)

FNphasing: a novel fast heuristic algorithm for haplotype phasing based on flow network model.
Yang J, Xu Y, Yao X, Chen G.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar 7. [Epub ahead of print]

Cost-effective and scalable DNA extraction method from dried blood spots.
Saavedra-Matiz CA, Isabelle JT, Biski CK, Duva SJ, et al.
Clin Chem. 2013 Mar 18. [Epub ahead of print]

CistromeFinder for ChIP-seq and DNase-seq data reuse.
Sun H, Qin B, Liu T, Wang Q, et al.
Bioinformatics. 2013 Mar 18. [Epub ahead of print]