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Recent Sequencing Papers of Note: Sep 2, 2014


SeqControl: process control for DNA sequencing.
Chong LC, Albuquerque MA, Harding NJ, Caloian C, et al.
Nat Methods. 2014 Aug 31. [Epub ahead of print]
(See our coverage of this paper here.)

Large scale comparison of non-human sequences in human sequencing data.
Tae H, Karunasena E, Bavarva JH, McIver LJ, Garner HR.
Genomics. 2014 Aug 27. [Epub ahead of print]

SeqCompress: an algorithm for biological sequence compression.
Sardaraz M, Tahir M, Ikram AA, Bajwa H.
Genomics. 2014 Aug 27. [Epub ahead of print]

An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer.
Katsuoka F, Yokozawa J, Tsuda K, Ito S, et al.
Anal Biochem. 2014 Aug 27. [Epub ahead of print]

poRe: an R package for the visualization and analysis of nanopore sequencing data.
Watson M, Thomson M, Risse J, Talbot R, et al.
Bioinformatics. 2014 Aug 29. [Epub ahead of print]

Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment.
Xiao X, Sogge H, Lagesen K, Tooming-Klunderud A, et al.
PLOS One. 2014 Aug 29;9(8):e106510.

Y chromosomes of 40% Chinese descend from three neolithic super-grandfathers.
Yan S, Wang CC, Zheng HX, Wang W, et al.
PLOS One. 2014 Aug 29;9(8):e105691.

The genetic prehistory of the New World Arctic.
Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, et al.
Science. 2014 Aug 29;345(6200):1255832.

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, et al.
Science. 2014 Aug 29;345(6200):1074-9.

Longitudinal analysis of microbial interaction between humans and the indoor environment.
Lax S, Smith DP, Hampton-Marcell J, Owens SM, et al.
Science. 2014 Aug 29;345(6200):1048-52.

RVboost: RNA-seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, et al.
Bioinformatics. 2014 Aug 27. [Epub ahead of print]

Exome sequence read depth methods for identifying copy number changes.
Kadalayil L, Rafiq S, Rose-Zerilli MJ, Pengelly RJ, et al.
Brief Bioinform. 2014 Aug 28. [Epub ahead of print]

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.
Ioannidis P, Lu Y, Kumar N, Creasy T, et al.
BMC Genomics. 2014 Aug 29;15(1):738.

Integrating dilution-based sequencing and population genotypes for single individual haplotyping.
Matsumoto H, Kiryu H.
BMC Genomics. 2014 Aug 28;15(1):733.

Measuring the activity of protein variants on a large scale using deep mutational scanning.
Fowler DM, Stephany JJ, Fields S.
Nat Protoc. 2014 Sep;9(9):2267-2284.

The genomic architecture of population divergence between subspecies of the European rabbit.
Carneiro M, Albert FW, Afonso S, Pereira RJ, et al.
PLOS Genet. 2014 Aug 28;10(8):e1003519.

LoRDEC: accurate and efficient long read error correction.
Salmela L, Rivals E.
Bioinformatics. 2014 Aug 26. [Epub ahead of print]

Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, et al.
Nature. 2014 Aug 28;512(7515):445-8.

Regulatory analysis of the C. elegans genome with spatiotemporal resolution.
Araya CL, Kawli T, Kundaje A, Jiang L, et al.
Nature. 2014 Aug 28;512(7515):400-5.

Improved variant calling accuracy by merging replicates in whole-exome sequencing studies.
Zhang Y, Li B, Li C, Cai Q, et al.
Biomed Res Int. 2014;2014:319534.

Determination of in vivo RNA kinetics using RATE-seq.
Neymotin B, Athanasiadou R, Gresham D.
RNA. 2014 Aug 26. [Epub ahead of print]

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
Bellos E, Coin LJ.
Bioinformatics. 2014 Sep 1;30(17):i639-i645.

Broad-Enrich: functional interpretation of large sets of broad genomic regions.
Cavalcante RG, Lee C, Welch RP, Patil S, et al.
Bioinformatics. 2014 Sep 1;30(17):i393-i400.

Probabilistic single-individual haplotyping.
Kuleshov V.
Bioinformatics. 2014 Sep 1;30(17):i379-i385.

Fiona: a parallel and automatic strategy for read error correction.
Schulz MH, Weese D, Holtgrewe M, Dimitrova V, et al.
Bioinformatics. 2014 Sep 1;30(17):i356-i363.

Alignment of high-throughput sequencing data inside in-memory databases.
Firnkorn D, Knaup-Gregori P, Lorenzo Bermejo J, Ganzinger M.
Stud Health Technol Inform. 2014;205:476-480.

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms.
Larsen PA, Heilman AM, Yoder AD.
BMC Genomics. 2014 Aug 26;15(1):720.

Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain.
Cai X, Evrony GD, Lehmann HS, Elhosary PC, et al.
Cell Rep. 2014 Aug 20. [Epub ahead of print]

Diversity and clonal selection in the human T-cell repertoire.
Qi Q, Liu Y, Cheng Y, Glanville J, et al.
Proc Natl Acad Sci U S A. 2014 Aug 25. [Epub ahead of print]

Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane.
Luan B, Zhou B, Huynh T, Zhou R.
Nanoscale. 2014 Aug 26. [Epub ahead of print]

Optimization of ELFSE DNA sequencing with EOF counterow and microuidics.
Fahrenkopf MA, Mukherjee T, Ydstie BE, Schneider JW.
Electrophoresis. 2014 Aug 25. [Epub ahead of print]

Practical barriers and ethical challenges in genetic data sharing.
Simpson CL, Goldenberg AJ, Culverhouse R, Daley D, et al.
Int J Environ Res Public Health. 2014 Aug 15;11(8):8383-8398.

Population clustering based on copy number variations detected from next generation sequencing data.
Duan J, Zhang JG, Wan M, Deng HW, Wang YP.
J Bioinform Comput Biol. 2014 Aug;12(4):1450021.

Forensic soil DNA analysis using high-throughput sequencing: A comparison of four molecular markers.
Young JM, Weyrich LS, Cooper A.
Forensic Sci Int Genet. 2014 Aug 4;13C:176-184.

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.
Wallberg A, Han F, Wellhagen G, Dahle B, et al.
Nat Genet. 2014 Aug 24. [Epub ahead of print]

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.
Wang C, Gong B, Bushel PR, Thierry-Mieg J, et al.
Nat Biotechnol. 2014 Aug 24. [Epub ahead of print]

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium; SEQC/MAQC-III Consortium.
Nat Biotechnol. 2014 Aug 24. [Epub ahead of print]
(See our coverage of this paper here.)

Detecting and correcting systematic variation in large-scale RNA sequencing data.
Li S, Labaj PP, Zumbo P, Sykacek P, et al.
Nat Biotechnol. 2014 Aug 24. [Epub ahead of print]

Normalization of RNA-seq data using factor analysis of control genes or samples.
Risso D, Ngai J, Speed TP, Dudoit S.
Nat Biotechnol. 2014 Aug 24. [Epub ahead of print]

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
Li S, Tighe SW, Nicolet CM, Grove D, et al.
Nat Biotechnol. 2014 Aug 24. [Epub ahead of print]
(See our coverage of this paper here.)

Using galaxy-P to leverage RNA-seq for the discovery of novel protein variations.
Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, et al.
BMC Genomics. 2014 Aug 22;15(1):703.

MT-Toolbox: improved amplicon sequencing using molecule tags.
Yourstone SM, Lundberg DS, Dangl JL, Jones CD.
BMC Bioinformatics. 2014 Aug 22;15(1):284.

Comparative analysis of functional metagenomic annotation and the mappability of short reads.
Carr R, Borenstein E.
PLOS One. 2014 Aug 22;9(8):e105776.

Single-molecule detection of a guanine(C8) - thymine(N3) cross-link using ion channel recording.
Wolna AH, Fleming AM, Burrows CJ.
J Phys Org Chem. 2014 Apr 1;27(4):247-251.

PyBamView: a browser based application for viewing short read alignments.
Gymrek M.
Bioinformatics. 2014 Aug 21. [Epub ahead of print]

Gene organization: nano-dissection and sequencing of DNA at single sub-nuclear structures.
Chen BK, Anchel D, Gong Z, Cotton R, et al.
Small. 2014 Aug;10(16):3266.