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In Print: Last Week's Sequencing-Related Papers of Note: Jan 15, 2013


Scotty: A web tool for designing RNA-seq experiments to measure differential gene expression.
Busby MA, Stewart C, Miller C, Grzeda K, Marth G.

Bioinformatics. 2013 Jan 12. [Epub ahead of print]

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets.
Breese MR, Liu Y.
Bioinformatics. 2013 Jan 12. [Epub ahead of print]

ViralFusionSeq: Accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
Li JW, Wan R, Yu CS, Co NN, et al.
Bioinformatics. 2013 Jan 12. [Epub ahead of print]

Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene.
Dubose AJ, Lichtenstein ST, Narisu N, Bonnycastle LL, et al.
Nucleic Acids Res. 2013 Jan 11. [Epub ahead of print]

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
Boitard S, Kofler R, Françoise P, Robelin D, et al.
Mol Ecol Resour. 2013 Jan 11. [Epub ahead of print]

Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction.
Lazinski DW, Camilli A.
Biotechniques. 2013 Jan;54(1):25-34.

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.
Mizrahi-Man O, Davenport ER, Gilad Y.
PLoS One. 2013;8(1):e53608.

Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.
Auburn S, Marfurt J, Maslen G, Campino S, et al.
PLoS One. 2013;8(1):e53160.

Reference-assisted chromosome assembly.
Kim J, Larkin DM, Cai Q, Asan, et al.
Proc Natl Acad Sci U S A. 2013 Jan 10. [Epub ahead of print]

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.
Costello M, Pugh TJ, Fennell TJ, Stewart C, et al.
Nucleic Acids Res. 2013 Jan 8. [Epub ahead of print]

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark S, Egan R, Frazier PI, Wang Z.
Bioinformatics. 2013 Jan 9. [Epub ahead of print]

Decombinator: a tool for fast, efficient gene assignment in T cell receptor sequences using a finite state machine.
Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B.
Bioinformatics. 2013 Jan 9. [Epub ahead of print]

SIBER: Systematic identification of bimodally expressed genes using RNAseq data.
Tong P, Chen Y, Su X, Coombes KR.
Bioinformatics. 2013 Jan 9. [Epub ahead of print]

Small RNA transcriptomes of two types of exosomes in human whole saliva determined by next generation sequencing.
Ogawa Y, Taketomi Y, Murakami M, Tsujimoto M, Yanoshita R.
Biol Pharm Bull. 2013;36(1):66-75.

Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P.
BMC Bioinformatics. 2012;13 Suppl 19:S10.

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
Chu HT, Hsiao WW, Tsao TT, Chang CM, et al.
BMC Genomics. 2012;13 Suppl 7:S5.

A fast and accurate algorithm for single individual haplotyping.
Xie M, Wang J, Jiang T.
vBMC Syst Biol. 2012;6 Suppl 2:S8.

Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.
Wang Y, Yu Y, Pan B, Hao P, et al.
BMC Syst Biol. 2012;6 Suppl 3:S21.

A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework.
Chang YJ, Chen CC, Chen CL, Ho JM.
BMC Genomics. 2012;13 Suppl 7:S28.

TranSeqAnnotator: large-scale analysis of transcriptomic data.
Menon R, Garg G, Gasser RB, Ranganathan S.
BMC Bioinformatics. 2012;13 Suppl 17:S24.

Combining multiple ChIP-seq peak detection systems using combinatorial fusion.
Schweikert C, Brown S, Tang Z, Smith PR, Hsu DF .
BMC Genomics. 2012;13 Suppl 8:S12.

DFI: gene feature discovery in RNA-seq experiments from multiple sources.
Ozer HG, Parvin JD, Huang K.
BMC Genomics. 2012;13 Suppl 8:S11.

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.
Zhou A, Breese MR, Hao Y, Edenberg HJ, et al.
BMC Genomics. 2012;13 Suppl 8:S10.

Palindromic sequence impedes sequencing-by-ligation mechanism.
Huang YF, Chen SC, Chiang YS, Chen TH, Chiu KP.
BMC Syst Biol. 2012;6 Suppl 2:S10.

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.
Yuan Y, Norris C, Xu Y, Tsui KW, et al.
BMC Genomics. 2012;13 Suppl 8:S9.

TIGER: tiled iterative genome assembler.
Wu XL, Heo Y, El Hajj I, Hwu WM, et al.
BMC Bioinformatics. 2012;13 Suppl 19:S18.

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data.
Liu Q, Guo Y, Li J, Long J, et al.
BMC Genomics. 2012;13 Suppl 8:S8.

Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes.
Trimarchi MP, Murphy M, Frankhouser D, Rodriguez BA, et al.
BMC Genomics. 2012;13 Suppl 8:S6.

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data.
Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, et al.
BMC Genomics. 2012;13 Suppl 7:S6.

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data.
Hayes M, Pyon YS, Li J.
PLoS One. 2012;7(12):e52881.

A comprehensive evaluation of alignment algorithms in the context of RNA-seq.
Lindner R, Friedel CC.
PLoS One. 2012;7(12):e52403.

Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumonia at single-base resolution.
Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, et al.
PLoS Genet. 2013 Jan;9(1):e1003191.

MaSC: Mappability-sensitive cross-correlation for estimating mean fragment length of single-end short read sequencing data.
Ramachandran P, Palidwor GA, Porter CJ, Perkins TJ.
Bioinformatics. 2013 Jan 7. [Epub ahead of print]

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang J, Lunyak VV, Jordan IK.
Bioinformatics. 2013 Jan 7. [Epub ahead of print]

RNA-seq based mapping and candidate identification of mutations from forward genetic screens.
Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB.
Genome Res. 2013 Jan 8. [Epub ahead of print]

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq.
Hill JT, Demarest BL, Bisgrove BW, Gorsi B, et al.
Genome Res. 2013 Jan 8. [Epub ahead of print]

Nascent-seq analysis of Drosophila cycling gene expression.
Rodriguez J, Tang CH, Khodor YL, Vodala S, et al.
Proc Natl Acad Sci U S A. 2013 Jan 7. [Epub ahead of print]

Genomic basis for coral resilience to climate change.
Barshis DJ, Ladner JT, Oliver TA, Seneca FO, et al.
Proc Natl Acad Sci U S A. 2013 Jan 7. [Epub ahead of print]

Structure-based whole genome realignment reveals many novel non-coding RNAs.
Will S, Yu M, Berger B.
Genome Res. 2013 Jan 7. [Epub ahead of print]

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
Wang Y, Lu J, Yu J, Gibbs RA, Yu F.
Genome Res. 2013 Jan 7. [Epub ahead of print]

An efficient rRNA removal method for RNA sequencing in GC-rich bacteria.
Peano C, Pietrelli A, Consolandi C, Rossi E, et al.
Microb Inform Exp. 2013 Jan 7;3(1):1. [Epub ahead of print]