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Last Week's Sequencing-Related Papers of Note: May 13, 2014


SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG, Hall IM.
Bioinformatics. 2014 May 7. [Epub ahead of print]

Probabilistic partitioning methods to find significant patterns in ChIP-seq data.
Nair NU, Kumar S, Moret BM, Bucher P.
Bioinformatics. 2014 May 7. [Epub ahead of print]

RNASeqGUI: a GUI for analysing RNA-seq data.
Russo F, Angelini C.
Bioinformatics. 2014 May 7. [Epub ahead of print]

Single-cell genomics for dissection of complex malaria infections.
Nair S, Nkhoma SC, Serre D, Zimmerman PA, et al.
Genome Res. 2014 May 8. [Epub ahead of print]

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.
Liang RH, Mo T, Dong W, Lee GQ, et al.
Nucleic Acids Res. 2014 May 7. [Epub ahead of print]

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Hach F, Sarrafi I, Hormozdiari F, Alkan C, et al.
Nucleic Acids Res. 2014 May 8. [Epub ahead of print]

A comparison of peak callers used for DNase-seq data.
Koohy H, Down TA, Spivakov M, Hubbard T.
PLoS One. 2014 May 8;9(5):e96303.

Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing.
Menzel U, Greiff V, Khan TA, Haessler U, et al.
PLoS One. 2014 May 8;9(5):e96727.

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.
Tome JM, Ozer A, Pagano JM, Gheba D, et al.
Nat Methods. 2014 May 8. [Epub ahead of print]

Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean iceman and the genetic structure of Europe.
Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, et al.
PLoS Genet. 2014 May 8;10(5):e1004353.

The tobacco genome sequence and its comparison with those of tomato and potato.
Sierro N, Battey JN, Ouadi S, Bakaher N, et al.
Nat Commun. 2014 May 8;5:3833.

SimRAD: a R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches.
Lepais O, Weir JT.
Mol Ecol Resour. 2014 May 7. [Epub ahead of print]

Comparative next-generation sequencing of adeno-associated virus inverted terminal repeats.
Petri K, Fronza R, Gabriel R, Käppel C, et al.
Biotechniques. 2014 May 1;56(5):269-73.

DNA translocation through short nanofluidic channels under asymmetric pulsed electric field.
Gupta C, Liao WC, Gallego-Perez D, Castro CE, Lee LJ.
Biomicrofluidics. 2014 Apr 16;8(2):024114.

Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing.
Zhan A, Xiong W, He S, Macisaac HJ.
PLoS One. 2014 May 6;9(5):e96928.

deepTools: a flexible platform for exploring deep-sequencing data.
Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T.
Nucleic Acids Res. 2014 May 5. [Epub ahead of print]

Nano-dissection and sequencing of DNA at single sub-nuclear structures.
Chen BK, Anchel D, Gong Z, Cotton R, et al.
Small. 2014 May 3. [Epub ahead of print]

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.
Shang J, Zhu F, Vongsangnak W, Tang Y, et al.
Biomed Res Int. 2014;2014:309650.

Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing.
Abusleme L, Hong BY, Dupuy AK, Strausbaugh LD, Diaz PI.
J Oral Microbiol. 2014 Apr 23;6.

Control of the conductance of engineered protein nanopores through concerted loop motions.
Zhuang T, Tamm LK.
Angew Chem Int Ed Engl. 2014 Apr 28. [Epub ahead of print]

Using next-generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate-synthase (ALS) based resistance in barnyard-grass, a polyploid grass weed.
Délye C, Causse R, Gautier V, Poncet C, Michel S.
Pest Manag Sci. 2014 Apr 28. [Epub ahead of print]

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Fort A, Hashimoto K, Yamada D, Salimullah M, et al.
Nat Genet. 2014 Apr 28. [Epub ahead of print]

PlasmidFinder and pMLST: in silico detection and typing of plasmids.
Carattoli A, Zankari E, Garcìa-Fernandez A, Volby Larsen M, et al.
Antimicrob Agents Chemother. 2014 Apr 28. [Epub ahead of print]

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for fecal and swab samples.
Vo AE, Jedlicka JA.
Mol Ecol Resour. 2014 Apr 29. [Epub ahead of print]

Single-molecule positioning in zeromode waveguides by DNA origami nano-adapters.
Pibiri E, Holzmeister P, Lalkens B, Acuna GP, Tinnefeld P.
Nano Lett. 2014 Apr 29. [Epub ahead of print]

Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA.
Zhao MT, Whyte JJ, Hopkins GM, Kirk MD, Prather RS.
Cell Reprogram. 2014 Apr 28. [Epub ahead of print]