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In Print: Last Week's Sequencing-Related Papers of Note: Jan 17, 2012

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Whole-genome sequence of Schistosoma haematobium.
Young ND, Jex AR, Li B, Liu S, et al.
Nat Genet. 2012 Jan 15. [Epub ahead of print]


Characterizing short read sequencing for gene discovery and RNA-seq analysis in Crassostrea gigas.
Gavery MR, Roberts SB.
Comp Biochem Physiol Part D Genomics Proteomics. 2011 Dec 29. [Epub ahead of print]


BarraCUDA — a fast short read sequence aligner using graphics processing units.
Klus P, Lam S, Lyberg D, Cheung MS, et al.
BMC Res Notes. 2012 Jan 13;5(1):27.


Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-seq.
Feng C, Chen M, Xu CJ, Bai L, et al.
BMC Genomics. 2012 Jan 13;13(1):19.


VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern.
Hu Q, Wang D, Yan L, Zhao H, Liu S.
BMC Res Notes. 2012 Jan 14;5(1):31.


Probing the SELEX process with next-generation sequencing.
Schütze T, Wilhelm B, Greiner N, Braun H, et al.
PLoS One. 2011;6(12):e29604.


Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks.
Kobayashi H, Sakurai T, Imai M, Takahashi N, et al.
PLoS Genet. 2012 Jan;8(1):e1002440.


A comprehensive transcriptome assembly of Pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms.
Kudapa H, Bharti AK, Cannon SB, Farmer AD, et al.
Mol Plant. 2012 Jan 11. [Epub ahead of print]


Developmental and insecticide-resistant insights from the de novo assembled transcriptome of the diamondback moth, Plutella xylostella.
He W, You M, Vasseur L, Yang G, et al.
Genomics. 2012 Jan 5. [Epub ahead of print]


Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR
sequencing.

Koepke T, Schaeffer S, Krishnan V, Jiwan D, et al.
BMC Genomics. 2012 Jan 12;13(1):18.


Customisation of the exome data analysis pipeline using a combinatorial approach.
Pattnaik S, Vaidyanathan S, Pooja DG, Deepak S, Panda B.
PLoS One. 2012;7(1):e30080.


SNP discovery and development of a high-density genotyping array for sunflower.
Bachlava E, Taylor CA, Tang S, Bowers JE, et al.
PLoS One. 2012;7(1):e29814.


IQSeq: Integrated isoform quantification analysis based on next-generation sequencing.
Du J, Leng J, Habegger L, Sboner A, et al.
PLoS One. 2012;7(1):e29175.


Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.
Emde AK, Schulz MH, Weese D, Sun R, et al.
Bioinformatics. 2012 Jan 11. [Epub ahead of print]


CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures.
Hentrich T, Schulze JM, Emberly E, Kobor MS.
Bioinformatics. 2012 Jan 11. [Epub ahead of print]


Analysis of high-throughput ancient DNA sequencing data.
Kircher M.
Methods Mol Biol. 2012;840:197-228.


Case study: enrichment of ancient mitochondrial DNA by hybridization capture.
Horn S.
Methods Mol Biol. 2012;840:189-95.


Case Study: targeted high-throughput sequencing of mitochondrial genomes from extinct cave bears via direct multiplex PCR sequencing (DMPS) .
Stiller M.
Methods Mol Biol. 2012;840:171-6.


Generating barcoded libraries for multiplex high-throughput sequencing.
Knapp M, Stiller M, Meyer M.
Methods Mol Biol. 2012;840:155-70.


Preparation of next-generation sequencing libraries from damaged DNA.
Briggs AW, Heyn P.
Methods Mol Biol. 2012;840:143-54.


Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples.
Mullen MP, Creevey CJ, Berry DP, McCabe MS, et al.
BMC Genomics. 2012 Jan 11;13(1):16.


Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.
Bizuayehu TT, Lanes CF, Furmanek T, Karlsen BO, et al.
BMC Genomics. 2012 Jan 10;13(1):11.


Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea.
Wu B, Li Y, Yan H, Ma Y, et al.
BMC Genomics. 2012 Jan 10;13(1):15.


Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
Klassen JL, Currie CR.
BMC Genomics. 2012 Jan 10;13(1):14.


Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.
Shiroguchi K, Jia TZ, Sims PA, Xie XS.
Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print]


De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.
Nat Genet. 2012 Jan 8. [Epub ahead of print]


Use of ChIP-seq data for the design of a multiple promoter-alignment method.
Erb I, González-Vallinas JR, Bussotti G, Blanco E, et al.
Nucleic Acids Res. 2012 Jan 9. [Epub ahead of print]


Quantitative interactor screening with next-generation sequencing (QIS-seq) identifies Arabidopsis thaliana MLO2 as a target of the Pseudomonas syringae type III effector HopZ2.
Lewis JD, Wan J, Ford R, Gong Y, et al.
BMC Genomics. 2012 Jan 9;13(1):8.


Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits.
Zuo J, Zhu B, Fu D, Zhu Y, et al.
BMC Genomics. 2012 Jan 9;13(1):7.


Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis).
Yu K, Xu Q, Da X, Guo F, et al.
BMC Genomics. 2012 Jan 10;13(1):10.


Slowing down DNA translocation through a nanopore in lithium chloride.
Kowalczyk SW, Wells DB, Aksimentiev A, Dekker C.
Nano Lett. 2012 Jan 9. [Epub ahead of print]

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