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In Print: Sequencing-Related Papers of Note of the Last Two Weeks: Jan 2, 2013


Simplifier: a web tool to eliminate redundant NGS contigs.
Ramos RT, Carneiro AR, Azevedo V, Schneider MP, et al.
Bioinformation. 2012;8(20):996-9.

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.
Szatkiewicz JP, Wang W, Sullivan PF, Wang W, Sun W .
Nucleic Acids Res. 2012 Dec 28. [Epub ahead of print]

Strand-specific libraries for high throughput RNA sequencing (RNA-seq) prepared without poly(A) selection.
Zhang Z, Theurkauf WE, Weng Z, Zamore PD.
Silence. 2012 Dec 28;3(1):9.

The genome of Prunus mume.
Zhang Q, Chen W, Sun L, Zhao F, et al.
Nat Commun. 2012 Dec 27;3:1318.

A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIP-seq data types.
Xing H, Liao W, Mo Y, Zhang MQ.
J Vis Exp. 2012 Dec 10;(70).

How deep is deep enough for RNA-seq profiling of bacterial transcriptomes?
Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J.
BMC Genomics. 2012 Dec 27;13(1):734.

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data.
Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R.
Nucleic Acids Res. 2012 Dec 24. [Epub ahead of print]

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity.
Yang C, Ji Y, Wang X, Yang C, Yu DW.
Sci China Life Sci. 2012 Dec 27. [Epub ahead of print]

Hap-seqX: Expedite algorithm for haplotype phasing with imputation using sequence data.
He D, Eskin E.
Gene. 2012 Dec 23. [Epub ahead of print]

Comparison of metagenomic samples using sequence signatures.
Jiang B, Song K, Ren J, Deng M, et al.
BMC Genomics. 2012 Dec 27;13(1):730.

SRmapper: A fast and sensitive genome-hashing alignment tool.
Gontarz PM, Berger J, Wong CF.
Bioinformatics. 2012 Dec 24. [Epub ahead of print]

Two methods for full-length RNA sequencing for low quantities of cells and single cells.
Pan X, Durrett RE, Zhu H, Tanaka Y, et al.
Proc Natl Acad Sci U S A. 2012 Dec 24. [Epub ahead of print]

Peak identification for ChIP-seq data with no controls.
Zhang YF, Su B.
Dongwuxue Yanjiu. 2012 Dec 8;33(E5-6):E121-E128.

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus).
Dong Y, Xie M, Jiang Y, Xiao N, et al.
Nat Biotechnol. 2012 Dec 23. [Epub ahead of print]

Insertion kinetics of small nucleotides through single walled carbon nanotube.
Clavier A, Kraszewski S, Ramseyer C, Picaud F.
J Biotechnol. 2012 Dec 19. [Epub ahead of print]

pH tuning of DNA translocation time through organically functionalized nanopores.
Anderson BN, Muthukumar M, Meller A.
ACS Nano. 2012 Dec 22. [Epub ahead of print]

HLA typing from RNA-seq sequence reads.
Boegel S, Lower M, Schafer M, Bukur T, et al.
Genome Med. 2012 Dec 22;4(12):102.

Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.
Genome Biol. 2012 Dec 22;13(12):R122.

cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.
Bellos E, Johnson MR, Coin LJ.
Genome Biol. 2012 Dec 22;13(12):R120.

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.
Lu T, Zhu C, Lu G, Guo Y, et al.
BMC Genomics. 2012 Dec 22;13(1):721.

Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing.
Lu S, Zong C, Fan W, Yang M, et al.
Science. 2012 Dec 21;338(6114):1627-30.

Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.
Zong C, Lu S, Chapman AR, Xie XS.
Science. 2012 Dec 21;338(6114):1622-6.
(See our coverage of this paper here.)

Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.
Zhang G, Cowled C, Shi Z, Huang Z, et al.
Science. 2012 Dec 20. [Epub ahead of print]

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing.
Ross JP, Shaw JM, Molloy PL.
Epigenetics. 2012 Dec 20;8(1). [Epub ahead of print]

Insights into bilaterian evolution from three spiralian genomes.
Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, et al.
Nature. 2012 Dec 19. [Epub ahead of print]

TrueSight: a new algorithm for splice junction detection using RNA-seq.
Li Y, Li-Byarlay H, Burns P, Borodovsky M, et al.
Nucleic Acids Res. 2012 Dec 18. [Epub ahead of print]

Insights from characterizing extinct human gut microbiomes.
Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, et al.
PLoS One. 2012;7(12):e51146.

RNA-seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering.
Sîrbu A, Kerr G, Crane M, Ruskin HJ.
PLoS One. 2012;7(12):e50986.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.
Mavromatis K, Land ML, Brettin TS, Quest DJ, et al.
PLoS One. 2012;7(12):e48837.

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method.
Zhou ZX, Zhang MJ, Peng X, Takayama Y, et al.
Genome Res. 2012 Dec 17. [Epub ahead of print]

High-throughput compression of FASTQ data with SeqDB.
Howison M.
IEEE/ACM Trans Comput Biol Bioinform. 2012 Dec 10. [Epub ahead of print]

Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets.
Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A.
Genomics. 2012 Dec 11. [Epub ahead of print]

MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case-control samples.
Aberg KA, McClay JL, Nerella S, Xie LY, et al.
Epigenomics. 2012 Dec;4(6):605-21.