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Last Week's Sequencing-Related Papers of Note: Feb 4, 2014


Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis.
Wagner DM, Klunk J, Harbeck M, Devault A, et al.
Lancet Infect Dis. 2014 Jan 27. [Epub ahead of print]

Finding the missing honey bee genes: lessons learned from a genome upgrade.
Elsik CG, Worley KC, Bennett AK, Beye M, et al.
BMC Genomics. 2014 Jan 30;15(1):86.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.
Bizon C, Spiegel M, Chasse SA, Gizer IR, et al.
BMC Genomics. 2014 Jan 30;15(1):85.

QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform.
Shrestha RK, Lubinsky B, Bansode VB, Moinz MB, et al.
BMC Bioinformatics. 2014 Jan 30;15(1):33.

Poly(A)-tail profiling reveals an embryonic switch in translational control.
Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP.
Nature. 2014 Jan 29. [Epub ahead of print]

SHEAR: sample heterogeneity estimation and assembly by reference.
Landman SR, Hwang TH, Silverstein KA, Li Y, et al.
BMC Genomics. 2014 Jan 29;15(1):84.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, et al.
BMC Bioinformatics. 2014 Jan 29;15(1):30.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.
Marine R, McCarren C, Vorrasane V, Nasko D, et al.
Microbiome. 2014 Jan 30;2(1):3.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.
David FP, Delafontaine J, Carat S, Ross FJ, et al.
PLOS One. 2014 Jan 27;9(1):e85879.

NGSANE: a lightweight production informatics framework for high throughput data analysis.
Buske FA, French HJ, Smith MA, Clark SJ, Bauer DC.
Bioinformatics. 2014 Jan 26. [Epub ahead of print]

Parseq: reconstruction of microbial transcription landscape from RNA-seq read counts using state-space models.
Mirauta B, Nicolas P, Richard H.
Bioinformatics. 2014 Jan 27. [Epub ahead of print]

CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Liu Y, Popp B, Schmidt B.
PLOS One. 2014 Jan 22;9(1):e86869.

PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing.
Li X, Chen S, Xie W, Vogel I, et al.
PLOS One. 2014 Jan 21;9(1):e85096.

Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system.
Shin S, Park J.
Nucleic Acids Res. 2014 Jan 23. [Epub ahead of print]

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.
Liu B, Li J, Liu C.
J Biomed Inform. 2014 Jan 22. [Epub ahead of print]

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3.

From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.
Clarke AC, Prost S, Stanton JA, White WT, et al.
BMC Genomics. 2014 Jan 25;15(1):68.