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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.