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Last Week's Sequencing-Related Papers of Note: Mar 11, 2014


An evaluation of copy number variation detection tools from whole-exome sequencing data.
Tan R, Wang Y, Kleinstein SE, Liu Y, et al.
Hum Mutat. 2014 Mar 5. [Epub ahead of print]

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
Lee WP, Stromberg MP, Ward A, Stewart C, et al.
PLOS One. 2014 Mar 5;9(3):e90581.

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data.
Alkodsi A, Louhimo R, Hautaniemi S.
Brief Bioinform. 2014 Mar 5. [Epub ahead of print]

Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species.
Ahmadvand R, Poczai P, Hajianfar R, Kolics B, et al.
Gene. 2014 Feb 26. [Epub ahead of print]

Genomics in premature infants: a non-invasive strategy to obtain high-quality DNA.
Said M, Cappiello C, Devaney JM, Podini D, et al.
Sci Rep. 2014 Mar 6;4:4286.

Impact of sequencing depth in ChIP-seq experiments.
Jung YL, Luquette LJ, Ho JW, Ferrari F, et al.
Nucleic Acids Res. 2014 Mar 5. [Epub ahead of print]

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing.
Mosen-Ansorena D, Telleria N, Veganzones S, De la Orden V, et al.
BMC Genomics. 2014 Mar 5;15(1):178.

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.
Yava G, Koyutürk M, Gould MP, McMahon S, Laframboise T.
BMC Genomics. 2014 Mar 5;15(1):175.

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.
Wen L, Li X, Yan L, Tan Y, et al.
Genome Biol. 2014 Mar 4;15(3):R49.

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
Yuan T, Huang X, Dittmar RL, Du M, et al.
BMC Genomics. 2014 Mar 5;15(1):176.

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization.
Qin C, Yu C, Shen Y, Fang X, et al.
Proc Natl Acad Sci U S A. 2014 Mar 3. [Epub ahead of print]

Simultaneous rapid sequencing of multiple RNA virus genomes.
Neill JD, Bayles DO, Ridpath JF.
J Virol Methods. 2014 Feb 28. [Epub ahead of print]

Ion transport in sub-5-nm graphene nanopores.
Suk ME, Aluru NR.
J Chem Phys. 2014 Feb 28;140(8):084707.

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
Glaubitz JC, Casstevens TM, Lu F, Harriman J, et al.
PLOS One. 2014 Feb 28;9(2):e90346.

Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing.
Smith DP, Peay KG.
PLOS One. 2014 Feb 28;9(2):e90234.

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.
Gray JM, Harmin DA, Boswell SA, Cloonan N, et al.
PLOS One. 2014 Feb 26;9(2):e89673.

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.
Xu G, Strong MJ, Lacey MR, Baribault C, et al.
PLOS One. 2014 Feb 25;9(2):e89445.

Normalization of RNA-sequencing data from samples with varying mRNA levels.
Aanes H, Winata C, Moen LF, Ostrup O, et al.
PLOS One. 2014 Feb 25;9(2):e89158.

A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature.
Marakeby H, Badr E, Torkey H, Song Y, et al.
PLOS One. 2014 Feb 21;9(2):e89142.

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.
Kennedy NA, Walker AW, Berry SH, Duncan SH, et al.
PLOS One. 2014 Feb 24;9(2):e88982.

Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.
Harper M, Gronenberg L, Liao J, Lee C.
PLOS One. 2014 Feb 26;9(2):e88072.

Accurate and robust prediction of genetic relationship from whole-genome sequences.
Li H, Glusman G, Huff C, Caballero J, Roach JC.
PLOS One. 2014 Feb 28;9(2):e85437.

Classic selective sweeps revealed by massive sequencing in cattle.
Qanbari S, Pausch H, Jansen S, Somel M, et al.
PLOS Genet. 2014 Feb 27;10(2):e1004148.

High-throughput sequencing reveals inbreeding depression in a natural population.
Hoffman JI, Simpson F, David P, Rijks JM, et al.
Proc Natl Acad Sci U S A. 2014 Feb 28. [Epub ahead of print]

Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis.
Briggs K, Kwok H, Tabard-Cossa V.
Small. 2014 Mar 2. [Epub ahead of print]

Graphene nanopore support system for simultaneous high resolution AFM imaging and conductance measurements.
Connelly L, Meckes B, Larkin J, Gillman AL, et al.
ACS Appl Mater Interfaces. 2014 Feb 28. [Epub ahead of print]

Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL.
Genome Biol. 2014 Mar 3;15(3):R46.

Community fingerprinting in a sequencing world.
van Dorst J, Bissett A, Palmer AS, Brown M, et al.
FEMS Microbiol Ecol. 2014 Mar 1. [Epub ahead of print]