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In Print: Last Week's Sequencing-Related Papers of Note: Apr 9, 2013


QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q, Su X, Wang A, Xu J, Ning K.
PLoS One. 2013;8(4):e60234.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, et al.
Genome Res. 2013 Apr 5. [Epub ahead of print]

Pyrosequencing analysis of the bacterial community in drinking water wells.
Navarro-Noya YE, Suárez-Arriaga MC, Rojas-Valdes A, Montoya-Ciriaco NM, et al.
Microb Ecol. 2013 Apr 6. [Epub ahead of print]

Multiplexed ionic current sensing with glass nanopores.
Bell NA, Thacker VV, Hernández-Ainsa S, Fuentes-Perez ME, et al.
Lab Chip. 2013 Apr 8. [Epub ahead of print]

Updating benchtop sequencing performance comparison.
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, et al.
Nat Biotechnol. 2013 Apr;31(4):294-6.
(See our coverage of this paper here.)

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.
Kelly AD, Hill KE, Correll M, Hu L, et al.
Genomics. 2013 Apr 2. [Epub ahead of print]

A tool for RNA sequencing sample identity check.
Huang J, Chen J, Lathrop M, Liang L.
Bioinformatics. 2013 Apr 4. [Epub ahead of print]

Single-molecule detection of 5-hydroxymethylcytosine in DNA through chemical modification and nanopore analysis.
Li WW, Gong L, Bayley H.
Angew Chem Int Ed Engl. 2013 Apr 4. [Epub ahead of print]

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.
Wan Y, Qu K, Ouyang Z, Chang HY.
Nat Protoc. 2013 Apr 4;8(5):849-69.

Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material.
Langevin SA, Bent ZW, Solberg OD, Curtis DJ, et al.
RNA Biol. 2013 Apr 1;10(4).

Probabilistic error correction for RNA sequencing.
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.
Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Liao Y, Smyth GK, Shi W.
Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.
Belova T, Zhan B, Wright J, Caccamo M, et al.
BMC Genomics. 2013 Apr 4;14(1):222.

PASTA: splice junction identification from RNA-sequencing data.
Tang S, Riva A.
BMC Bioinformatics. 2013 Apr 4;14(1):116.

Identification of SNPs in closely related temperate japonica rice cultivars using restriction enzyme-phased sequencing.
Kim SI, Tai TH.
PLoS One. 2013;8(3):e60176.

RNA-seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
Fan H, Xiao Y, Yang Y, Xia W, et al.
PLoS One. 2013;8(3):e59997.

Multiple single-cell genomes provide insight into functions of uncultured deltaproteobacteria in the human oral cavity.
Campbell AG, Campbell JH, Schwientek P, Woyke T, et al.
PLoS One. 2013;8(3):e59361.

Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 genomes data.
Quinn EM, Cormican P, Kenny EM, Hill M, et al.
PLoS One. 2013;8(3):e58815.

State-of-the-art fusion-finder algorithms sensitivity and specificity.
Carrara M, Beccuti M, Lazzarato F, Cavallo F, et al.
Biomed Res Int. 2013;2013:340620.

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
De Meyer T, Mampaey E, Vlemmix M, Denil S, et al.
PLoS One. 2013;8(3):e59068.

A method to detect differentially methylated loci with next-generation sequencing.
Xu H, Podolsky RH, Ryu D, Wang X, et al.
Genet Epidemiol. 2013 Apr 1. [Epub ahead of print]

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.
Xie G, Wang L, Gao Q, Yu W, et al.
J Sci Food Agric. 2013 Jan 19. [Epub ahead of print]

First insights into the metagenome of Egyptian mummies using next-generation sequencing.
Khairat R, Ball M, Chang CC, Bianucci R, et al.
J Appl Genet. 2013 Apr 4. [Epub ahead of print]

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription.
Vilfan ID, Tsai YC, Clark TA, Wegener J, et al.
J Nanobiotechnology. 2013 Apr 3;11(1):8.

The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome.
Moghadam HK, Harrison PW, Zachar G, Székely T, Mank JE.
Mol Ecol Resour. 2013 Mar 29. [Epub ahead of print]

Whole-exome targeted sequencing of the uncharacterized pine genome.
Neves LG, Davis JM, Brad Barbazuk W, Kirst M.
Plant J. 2013 Apr 4. [Epub ahead of print]

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling.
Arnold B, Corbett-Detig RB, Hartl D, Bomblies K.
Mol Ecol. 2013 Apr 3. [Epub ahead of print]

PRICE: software for the targeted assembly of components of (meta)genomic sequence data.
Ruby JG, Bellare P, Derisi JL.
G3 (Bethesda). 2013 Mar 23. [Epub ahead of print]

The genomic and transcriptomic landscape of a HeLa cell line.
Landry JJ, Pyl PT, Rausch T, Zichner T, et al.
G3 (Bethesda). 2013 Mar 26. [Epub ahead of print]

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks.
Kitano J, Yoshida K, Suzuki Y.
BMC Genomics. 2013 Apr 2;14(1):214.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.
Kisand V, Lettieri T.
BMC Genomics. 2013 Apr 1;14(1):211.