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In Print: Last Week's Sequencing-Related Papers of Note: Jul 24, 2012

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MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Nucleic Acids Res. 2012 Jul 19. [Epub ahead of print]


Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions.
Nolte-'t Hoen EN, Buermans HP, Waasdorp M, Stoorvogel W, et al.
Nucleic Acids Res. 2012 Jul 19. [Epub ahead of print]


Joint genotype calling with array and sequence data.
O'Connell J, Marchini J.
Genet Epidemiol. 2012 Jul 20. [Epub ahead of print]


Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.
Sherstnev A, Duc C, Cole C, Zacharaki V, et al.
Nat Struct Mol Biol. 2012 Jul 22. [Epub ahead of print]


Denaturation mapping of Saccharomyces cerevisiae.
Welch RL, Sladek R, Dewar K, Reisner WW.
Lab Chip. 2012 Jul 23. [Epub ahead of print]


SpliceSeq: a resource for analysis and visualization of RNA-seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.
Bioinformatics. 2012 Jul 20. [Epub ahead of print]


Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm.
Wang J, Fan HC, Behr B, Quake SR.
Cell. 2012 Jul 20;150(2):402-12.
(See our coverage of this paper here.)


Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions.
Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, et al.
Cell. 2012 Jul 20;150(2):279-90.


Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.
Meglécz E, Nève G, Biffin E, Gardner MG.
PLoS One. 2012;7(7):e40861.


Quantifying uniformity of mapped reads.
Hower V, Starfield R, Roberts A, Pachter L.
Bioinformatics. 2012 Jul 18. [Epub ahead of print]


Fast and accurate read alignment for resequencing.
Mu JC, Jiang H, Kiani A, Mohiyuddin M, et al.
Bioinformatics. 2012 Jul 18. [Epub ahead of print]


Analysis of context-dependent errors for Illumina sequencing.
Abnizova I, Leonard S, Skelly T, Brown A, et al.
J Bioinform Comput Biol. 2012 Apr;10(2):1241005.


Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.
Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.
BMC Bioinformatics. 2012 Jul 18;13(1):170.


Electrokinetic ion and fluid transport in nanopores functionalized by polyelectrolyte brushes.
Yeh LH, Zhang M, Hu N, Joo SW, et al.
Nanoscale. 2012 Jul 17. [Epub ahead of print]


Paired-end sequencing of fosmid libraries by Illumina.
Williams LJ, Tabbaa DG, Li N, Berlin AM, et al.
Genome Res. 2012 Jul 16. [Epub ahead of print]


Slim-Filter: an interactive windows-based application for Illumina Genome Analyzer data assessment and manipulation.
Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, et al.
BMC Bioinformatics. 2012 Jul 16;13(1):166.


Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes.
Pilloni G, Granitsiotis MS, Engel M, Lueders T.
PLoS One. 2012;7(7):e40467.


Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma.
Jiang Y, Soong TD, Wang L, Melnick AM, Elemento O.
PLoS One. 2012;7(7):e40332.


Efficiency and power as a function of sequence coverage, SNP array density, and imputation.
Flannick J, Korn JM, Fontanillas P, Grant GB, et al.
PLoS Comput Biol. 2012 Jul;8(7):e1002604.


Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.
Yang H, Tao Y, Zheng Z, Li C, et al.
BMC Genomics. 2012 Jul 17;13(1):318.


Measurement of the docking time of a DNA molecule onto a solid-state nanopore.
Kowalczyk SW, Dekker C.
Nano Lett. 2012 Jul 17. [Epub ahead of print]


Human gut microbiome viewed across age and geography.
Yatsunenko T, Rey FE, Manary MJ, Trehan I, et al.
Nature. 2012 May 9;486(7402):222-7.

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