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Recent Sequencing-Related Papers of Note: Oct 21, 2014


Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.
Amini S, Pushkarev D, Christiansen L, Kostem E, et al.
Nat Genet. 2014 Oct 19. [Epub ahead of print]

Comprehensive variation discovery in single human genomes.
Weisenfeld NI, Yin S, Sharpe T, Lau B, et al.
Nat Genet. 2014 Oct 19. [Epub ahead of print]

Transcriptomic portrait of human mesenchymal stromal/stem cells isolated from bone marrow and placenta.
Roson-Burgo B, Sanchez-Guijo F, Del Cañizo C, De Las Rivas J.
BMC Genomics. 2014 Oct 19;15(1):910.

Bison: bisulfite alignment on nodes of a cluster.
Ryan DP, Ehninger D.
BMC Bioinformatics. 2014 Oct 18;15(1):337.

Sequence assembly using next generation sequencing data-challenges and solutions.
Chin FY, Leung HC, Yiu SM.
Sci China Life Sci. 2014 Oct 17. [Epub ahead of print]

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.
Sathe C, Girdhar A, Leburton JP, Schulten K.
Nanotechnology. 2014 Oct 17;25(44):445105.

Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging.
Miura F, Ito T.
DNA Res. 2014 Oct 16. [Epub ahead of print]

SraTailor: graphical user interface software for processing and visualizing ChIP-seq data.
Oki S, Maehara K, Ohkawa Y, Meno C.
Genes Cells. 2014 Oct 17. [Epub ahead of print]

Rcount: simple and flexible RNA-seq read counting.
Schmid MW, Grossniklaus U.
Bioinformatics. 2014 Oct 15. [Epub ahead of print]

miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.
Jang I, Chang H, Jun Y, Park S, et al.
Bioinformatics. 2014 Oct 15. [Epub ahead of print]

Detection of internal exon deletion with exon Del.
Guo Y, Zhao S, Lehmann BD, Sheng Q, et al.
BMC Bioinformatics. 2014 Oct 16;15(1):332.

A new rhesus macaque assembly and annotation for next-generation sequencing analyses.
Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, et al.
Biol Direct. 2014 Oct 14;9(1):20.

Questioning the prevalence and reliability of human mitochondrial DNA heteroplasmy from massively parallel sequencing data.
Just RS, Irwin JA, Parson W.
Proc Natl Acad Sci U S A. 2014 Oct 15. [Epub ahead of print]

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice.
Greiff V, Menzel U, Haessler U, Cook SC, et al.
BMC Immunol. 2014 Oct 16;15(1):40.

Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City.
Firth C, Bhat M, Firth MA, Williams SH, et al.
MBio. 2014 Oct 14;5(5).

Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment.
Scott JG, Warren WC, Beukeboom LW, Bopp D, et al.
Genome Biol. 2014 Oct 14;15(10):466.

Facilitated sequence counting and assembly by template mutagenesis.
Levy D, Wigler M.
Proc Natl Acad Sci U S A. 2014 Oct 13. [Epub ahead of print]

Comparing high-throughput platforms for sequencing the V4 region of SSU-rDNA in environmental microbial eukaryotic diversity surveys.
Mahé F, Mayor J, Bunge J, Chi J, et al.
J Eukaryot Microbiol. 2014 Oct 14. [Epub ahead of print]

Next-generation sequencing of custom amplicons to improve coverage of HaloPlex multigene panels.
Coonrod EM, Durtschi JD, Webb CV, Voelkerding KV, Kumánovics A.
Biotechniques. 2014 Oct 1;57(4):204-7.

A kinetic model-based algorithm to classify NGS short reads by their allele origin.
Marinoni A, Rizzo E, Limongelli I, Gamba P, Bellazzi R.
J Biomed Inform. 2014 Oct 10. [Epub ahead of print]

Controlling polymer translocation and ion transport via charge correlations.
Buyukdagli S, Ala-Nissila T.
Langmuir. 2014 Oct 13. [Epub ahead of print]

A comparison of control samples for ChIP-seq of histone modifications.
Flensburg C, Kinkel SA, Keniry A, Blewitt ME, Oshlack A.
Front Genet. 2014 Sep 25;5:329.