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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]