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Recent Sequencing-Related Papers of Note: Oct 7, 2014


CompMap: a reference-based compression program to speed up read mapping to related reference sequences.
Zhu Z, Li L, Zhang Y, Yang Y, Yang X.
Bioinformatics. 2014 Oct 4. [Epub ahead of print]

A SNaPshot of next generation sequencing for forensic SNP analysis.
Daniel R, Santos C, Phillips C, Fondevila M, et al.
Forensic Sci Int Genet. 2014 Aug 30;14C:50-60.

Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.
Bragalini C, Ribière C, Parisot N, Vallon L, et al.
DNA Res. 2014 Oct 3. [Epub ahead of print]

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.
Ameur A, Bunikis I, Enroth S, Gyllensten U.
Database (Oxford). 2014 Oct 3;2014.

iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries.
Andersen JC, Mills NJ.
BMC Genomics. 2014 Oct 4;15(1):858.

Biogeography and individuality shape function in the human skin metagenome.
Oh J, Byrd AL, Deming C, Conlan S, et al.
Nature. 2014 Oct 1;514(7520):59-64.

A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-seq in a non-model bird.
Finseth FR, Harrison RG.
PLOS One. 2014 Oct 3;9(10):e108550.

Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy.
Bouwman AC, Veerkamp RF.
BMC Genet. 2014 Oct 3;15(1):105.

Performance of statistical methods on CHARGE targeted sequencing data.
Xing C, Dupuis J, Cupples L.
BMC Genet. 2014 Oct 3;15(1):104.

Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank) .
Tsangaras K, Wales N, Sicheritz-Pontén T, Rasmussen S, et al.
PLOS One. 2014 Oct 2;9(10):e109101.

Assessing T cell clonal size distribution: a non-parametric approach.
Bolkhovskaya OV, Zorin DY, Ivanchenko MV.
PLOS One. 2014 Oct 2;9(10):e108658.

PROPER: comprehensive power evaluation for differential expression using RNA-seq.
Wu H, Wang C, Wu Z.
Bioinformatics. 2014 Oct 1. [Epub ahead of print]

Alignathon: a competitive assessment of whole genome alignment methods.
Earl D, Nguyen NK, Hickey G, Harris RS, et al.
Genome Res. 2014 Oct 1. [Epub ahead of print]

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FS, et al.
Nucleic Acids Res. 2014 Sep 30. [Epub ahead of print]

BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high throughput sequencing data.
Chae H, Rhee S, Nephew KP, Kim S.
Bioinformatics. 2014 Sep 29. [Epub ahead of print]

Consensus genotyper for exome sequencing (CGES): improving the quality of exome variant genotypes.
Trubetskoy V, Rodriguez A, Dave U, Campbell N, et al.
Bioinformatics. 2014 Sep 29. [Epub ahead of print]

Improved assemblies using a source-agnostic pipeline for metagenomic assembly by merging (MeGAMerge) of contigs.
Scholz M, Lo CC, Chain PS.
Sci Rep. 2014 Oct 1;4:6480.

Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation.
Schlötterer C, Kofler R, Versace E, Tobler R, Franssen SU.
Heredity (Edinb). 2014 Oct 1;0. [Epub ahead of print]

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads.
Gouin A, Legeai F, Nouhaud P, Whibley A, et al.
Heredity. 2014 Oct 1. [Epub ahead of print]

RNA-seq gene profiling − a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A.
PLOS One. 2014 Sep 30;9(9):e107026.

Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli.
Thomason MK, Bischler T, Eisenbart SK, Förstner KU, et al.
J Bacteriol. 2014 Sep 29. [Epub ahead of print]

NSIT: Novel Sequence Identification Tool.
Pupacdi B, Javed A, Zaki MJ, Ruchirawat M.
PLOS One. 2014 Sep 29;9(9):e108011.

Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater.
Aw TG, Howe A, Rose JB.
J Virol Methods. 2014 Sep 25. [Epub ahead of print]

Parallel barcoding of antibodies for DNA-assisted proteomics.
Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A.
Proteomics. 2014 Sep 29. [Epub ahead of print]

The complex task of choosing a de novo assembly: Lessons from fungal genomes.
Gallo JE, Muñoz JF, Misas E, McEwen JG, Clay OK.
Comput Biol Chem. 2014 Aug 29. [Epub ahead of print]

The Scan

Cancer Survival Linked to Mutational Burden in Pan-Cancer Analysis

A pan-cancer paper appearing in JCO Precision Oncology suggests tumor mutation patterns provide clues for predicting cancer survival that are independent of other prognostic factors.

Australian Survey Points to Public Support for Genetic Risk Disclosure in Relatives of At-Risk Individuals

A survey in the European Journal of Human Genetics suggests most adult Australians are in favor of finding out if a relative tests positive for a medically actionable genetic variant.

Study Links Evolution of Stony Coral Skeleton to Bicarbonate Transporter Gene

A PNAS paper focuses on a skeleton-related bicarbonate transporter gene introduced to stony coral ancestors by tandem duplication.

Hormone-Based Gene Therapy to Sterilize Domestic Cat

A new paper in Nature Communication suggests that gene therapy could be a safer alternative to spaying domestic cats.