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Recent Sequencing-Related Papers of Note: Oct 14, 2014


Pooled assembly of marine metagenomic data sets: enriching annotation through chimerism.
Magasin JD, Gerloff DL.
Bioinformatics. 2014 Oct 11. [Epub ahead of print]

Estimating genotype error rates from high-coverage next-generation sequence data.
Wall JD, Tang LF, Zerbe B, Kvale MN, et al.
Genome Res. 2014 Oct 10. [Epub ahead of print]

Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.
Cao CC1, Sun X.
Bioinformatics. 2014 Oct 9. [Epub ahead of print]

SHAPE-seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing.
Loughrey D, Watters KE, Settle AH, Lucks JB.
Nucleic Acids Res. 2014 Oct 10. [Epub ahead of print]

Detecting ultralow-frequency mutations by duplex sequencing.
Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, et al.
Nat Protoc. 2014 Nov;9(11):2586-2606.

OncoCis: annotation of cis- regulatory mutations in cancer.
Perera D, Chacon D, Thoms J, Poulos RC, et al.
Genome Biol. 2014 Oct 9;15(10):485.

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.
Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S.
BMC Genomics. 2014 Oct 9;15(1):881.

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.
Shankla M, Aksimentiev A.
Nat Commun. 2014 Oct 9;5:5171.

Cassava genome from a wild ancestor to cultivated varieties.
Wang W, Feng B, Xiao J, Xia Z, et al.
Nat Commun. 2014 Oct 10;5:5110.

Enabling large-scale next-generation sequence assembly with Blacklight.
Couger MB, Pipes L, Squina F, Prade R, et al.
Concurr Comput. 2014 Sep 10;26(13):2157-2166.

Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.
Tang M, Tan M, Meng G, Yang S, et al.
Nucleic Acids Res. 2014 Oct 7. [Epub ahead of print]

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı GG, Frank CL, Crawford GE, Ohler U.
Nucleic Acids Res. 2014 Oct 7. [Epub ahead of print]

MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.
Zou D, Sun S, Li R, Liu J, et al.
Nucleic Acids Res. 2014 Oct 7. [Epub ahead of print]

Svaseq: removing batch effects and other unwanted noise from sequencing data.
Leek JT.
Nucleic Acids Res. 2014 Oct 7. [Epub ahead of print]

Randomized open-label pilot study of the influence of probiotics and the gut microbiome on toxic metal levels in Tanzanian pregnant women and school children.
Bisanz JE, Enos MK, Mwanga JR, Changalucha J, et al.
MBio. 2014 Oct 7;5(5).

Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs.
Pistis G, Porcu E, Vrieze SI, Sidore C, et al.
Eur J Hum Genet. 2014 Oct 8. [Epub ahead of print]

MUSIC: Identification of enriched regions in ChIP-seq experiments using a mappability-corrected multiscale signal processing framework.
Harmanci A, Rozowsky J, Gerstein M.
Genome Biol. 2014 Oct 8;15(10):474.

GroopM: an automated tool for the recovery of population genomes from related metagenomes.
Imelfort M, Parks D, Woodcroft BJ, Dennis P, et al.
PeerJ. 2014 Sep 30;2:e603.

Detailed comparison of two popular variant calling packages for exome and targeted exon studies.
Warden CD, Adamson AW, Neuhausen SL, Wu X.
PeerJ. 2014 Sep 30;2:e600.

Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.
Bao R, Huang L, Andrade J, Tan W, et al.
Cancer Inform. 2014 Sep 21;13(Suppl 2):67-82.

Detection of very long antisense transcripts by whole transcriptome RNA-seq analysis of Listeria monocytogenes by semiconductor sequencing technology.
Wehner S, Mannala GK, Qing X, Madhugiri R, et al.
PLoS One. 2014 Oct 6;9(10):e108639.

An iteration normalization and test method for differential expression analysis of RNA-seq data.
Zhou Y, Lin N, Zhang B.
BioData Min. 2014 Aug 13;7:15.

Precise and efficient antibody epitope determination through library design, yeast display and next generation sequencing.
Van Blarcom T, Rossi A, Foletti D, Sundar P, et al.
J Mol Biol. 2014 Oct 2. [Epub ahead of print]

IUTA: a tool for effectively detecting differential isoform usage from RNA-seq data.
Niu L, Huang W, Umbach DM, Li L.
BMC Genomics. 2014 Oct 6;15(1):862.