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Last Week's Sequencing-Related Papers of Note: Mar 18, 2014


Lacking alignments? The next generation sequencing mapper segemehl revisited.
Otto C, Stadler PF, Hoffmann S.
Bioinformatics. 2014 Mar 13. [Epub ahead of print]

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
Hoeppner MP, Lundquist A, Pirun M, Meadows JR, et al.
PLOS One. 2014 Mar 13;9(3):e91172.

Analysis options for high-throughput sequencing in miRNA expression profiling.
Stokowy T, Eszlinger M, Wierniak M, Fujarewicz K, et al.
BMC Res Notes. 2014 Mar 13;7(1):144.

Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.
Lu Z, Matera AG.
Nucleic Acids Res. 2014 Mar 12. [Epub ahead of print]

Orione, a web-based framework for NGS analysis in microbiology.
Cuccuru G, Orsini M, Pinna A, Sbardellati A, et al.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

Turtle: Identifying frequent k-mers with cache-efficient algorithms.
Roy RS, Bhattacharya D, Schliep A.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
Vander Heiden JA, Yaari G, Uduman M, Stern JN, et al.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

Genomewide, quantitative analysis of DNA methylation from bisulfite sequencing data.
Akman K, Haaf T, Gravina S, Vijg J, Tresch A.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

A gradient boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y, Li B, Tan R, Zhu X, Wang Y.
Bioinformatics. 2014 Mar 10. [Epub ahead of print]

Sequence capture using PCR-generated probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms.
Peñalba JV, Smith LL, Tonione MA, Sass C, et al.
Mol Ecol Resour. 2014 Mar 11. [Epub ahead of print]

Target enrichment using parallel nanoliter quantitative PCR amplification.
De Wilde B, Lefever S, Dong W, Dunne J, et al.
BMC Genomics. 2014 Mar 10;15(1):184.

Shotgun microbial profiling of fossil remains.
Der Sarkissian C, Ermini L, Jónsson H, Alekseev AN, et al.
Mol Ecol. 2014 Feb 12. [Epub ahead of print]

A robust approach for blind detection of balanced chromosomal rearrangements with whole-genome low-coverage sequencing.
Dong Z, Jiang L, Yang C, Hu H, et al.
Hum Mutat. 2014 Mar 7. [Epub ahead of print]

PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information.
Wu H, Ji H.
PLOS One. 2014 Mar 7;9(3):e89694.

Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.
Star B, Nederbragt AJ, Hansen MH, Skage M, et al.
PLOS One. 2014 Mar 7;9(3):e89676.

Qualifying high-throughput immune repertoire sequencing.
Niklas N, Pröll J, Weinberger J, Zopf A, et al.
Cell Immunol. 2014 Feb 23;288(1-2):31-38.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.
de Andrade RR, Vaslin MF.
Virol J. 2014 Mar 7;11(1):45.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.