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Last Week's Sequencing-Related Papers of Note: Jan 21, 2014


XS: a FASTQ read simulator.
Pratas DR, Pinho AJ, Rodrigues JM.
BMC Res Notes. 2014 Jan 16;7(1):40.

Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants.
Hunter CT, Suzuki M, Saunders J, Wu S, et al.
Front Plant Sci. 2014 Jan 7;4:545.

The locust genome provides insight into swarm formation and long-distance flight.
Wang X, Fang X, Yang P, Jiang X, et al.
Nat Commun. 2014 Jan 14;5:2957.

Technical variations in low-input RNA-seq methodologies.
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S.
Sci Rep. 2014 Jan 14;4:3678.

Reconstructing complex regions of genomes using long-read sequencing technology.
Huddleston J, Ranade S, Malig M, Antonacci F, et al.
Genome Res. 2014 Jan 13. [Epub ahead of print]

Whole genome sequence of a Turkish individual.
Dogan H, Can H, Otu HH.
PLoS One. 2014 Jan 9;9(1):e85233.

Transforming RNA-seq data to improve the performance of prognostic gene signatures.
Zwiener I, Frisch B, Binder H.
PLoS One. 2014 Jan 8;9(1):e85150.

An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments.
Duitama J, Quintero JC, Cruz DF, Quintero C, et al.
Nucleic Acids Res. 2014 Jan 11. [Epub ahead of print]

BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.
Ye C, Hsiao C, Bravo HC.
Bioinformatics. 2014 Jan 9. [Epub ahead of print]

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.
Lovatt D, Ruble BK, Lee J, Dueck H, et al.
Nat Methods. 2014 Jan 12. [Epub ahead of print]

Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58.
Wang X, Li Y, Ni T, Xie X, et al.
Cell Biosci. 2014 Jan 13;4(1):5.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.