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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

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.