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Recent Sequencing Papers of Note: Sep 9, 2014


Using Mendelian inheritance to improve high throughput SNP discovery.
Chen N, Van Hout CV, Gottipati S, Clark AG.
Genetics. 2014 Sep 5. [Epub ahead of print]

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary.
Molnár J, Nagy T, Stéger V, Tóth G, et al.
BMC Genomics. 2014 Sep 5;15(1):761.

Data analysis for 16S microbial profiling from different benchtop sequencing platforms.
Pylro VS, Roesch LF, Morais DK, Clark IM, et al.
J Microbiol Methods. 2014 Sep 2. [Epub ahead of print]

SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-seq signal profiles.
Wong KC, Li Y, Peng C, Zhang Z.
Bioinformatics. 2014 Sep 5. [Epub ahead of print]

Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Chiba K, Shiraishi Y, Nagata Y, Yoshida K, et al.
Bioinformatics. 2014 Sep 4. [Epub ahead of print]

mod_bio: Apache modules for next generation sequencing data.
Lindenbaum P, Redon R.
Bioinformatics. 2014 Sep 4. [Epub ahead of print]

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
Card DC, Schield DR, Reyes-Velasco J, Fujita MK, et al.
PLOS One. 2014 Sep 5;9(9):e106649.

Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.
Li X, Battle A, Karczewski KJ, Zappala Z, et al.
Am J Hum Genet. 2014 Sep 4;95(3):245-256.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Ahola V, Lehtonen R, Somervuo P, Salmela L, et al.
Nat Commun. 2014 Sep 5;5:4737.

subSeq: Determining appropriate sequencing depth through efficient read subsampling.
Robinson DG, Storey JD.
Bioinformatics. 2014 Sep 3. [Epub ahead of print]

Complete genome sequence of Pelosinus sp. strain UFO1 assembled using single-molecule real-time DNA sequencing technology.
Brown SD, Utturkar SM, Magnuson TS, Ray AE, et al.
Genome Announc. 2014 Sep 4;2(5).

Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods.
Bashford-Rogers RJ, Palser AL, Idris SF, Carter L, et al.
BMC Immunol. 2014 Aug 5;15(1):29.

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.
McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, et al.
PLOS One. 2014 Sep 4;9(9):e106689.

Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol.
DaCosta JM, Sorenson MD.
PLOS One. 2014 Sep 4;9(9):e106713.

MICO: A meta-tool for prediction of the effects of non-synonymous mutations.
Lee G, Chen CF.
Bioinformation. 2014 Jul 22;10(7):469-71.

A first look at the Oxford Nanopore MinION sequencer.
Mikheyev AS, Tin MM.
Mol Ecol Resour. 2014 Sep 3. [Epub ahead of print]
(See our coverage of this paper here.)

The genomic substrate for adaptive radiation in African cichlid fish.
Brawand D, Wagner CE, Li YI, Malinsky M, et al.
Nature. 2014 Sep 3. [Epub ahead of print]

A fault-tolerant method for HLA typing with PacBio data.
Chang CJ, Chen PL, Yang WS, Chao KM.
BMC Bioinformatics. 2014 Sep 3;15(1):296.

Comparing computational methods for identification of allele-specific expression based on next generation sequencing data.
Liu Z, Yang J, Xu H, Li C, et al.
Genet Epidemiol. 2014 Sep 2. [Epub ahead of print]

Utilizing next-generation sequencing to study homeologous polymorphisms and herbicide resistance endowing mutations in Poa annua acetolactate synthase genes.
Chen S, McElroy JS, Flessner ML, Dane F.
Pest Manag Sci. 2014 Sep 2. [Epub ahead of print]

Differential motif enrichment analysis of paired ChIP-seq experiments.
Lesluyes T, Johnson J, Machanick P, Bailey TL.
BMC Genomics. 2014 Sep 2;15(1):752.

Application of OmpF nanochannel forming protein in polynucleotide sequence recognition.
Hadi-Alijanvand S, Mobasheri H, Hadi-Alijanvand H.
J Mol Recognit. 2014 Oct;27(10):575-87.

H3K4me3 epigenomic landscape derived from ChIP-seq of 1,000 mouse early embryonic cells.
Shen J, Jiang D, Fu Y, Wu X, et al.
Cell Res. 2014 Sep 2. [Epub ahead of print]

Detection of aneuploidy from single fetal nucleated red blood cells using whole genome sequencing.
Hua R, Barrett AN, Tan TZ, Huang Z, et al.
Prenat Diagn. 2014 Sep 1. [Epub ahead of print]

PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.
Frankhouser DE, Murphy M, Blachly JS, Park J, et al.
Bioinformatics. 2014 Aug 31. [Epub ahead of print]

VirVarSeq: a low frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.
Verbist BM, Thys K, Reumers J, Wetzels Y, et al.
Bioinformatics. 2014 Aug 31. [Epub ahead of print]

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.
Rideout JR, He Y, Navas-Molina JA, Walters WA, et al.
PeerJ. 2014 Aug 21;2:e545.

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.
Lim YW, Cuevas DA, Silva GG, Aguinaldo K, et al.
PeerJ. 2014 Aug 19;2:e520.

Comparative evaluation of DNase-seq footprint identification strategies.
Barozzi I, Bora P, Morelli MJ.
Front Genet. 2014 Aug 15;5:278.

Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes.
Fang X, Seim I, Huang Z, Gerashchenko MV,
Cell Rep. 2014 Aug 27. [Epub ahead of print]

Genotyping by sequencing for genomic prediction in a soybean breeding population.
Jarquín D, Kocak K, Posadas L, Hyma K, et al.
BMC Genomics. 2014 Aug 29;15(1):740.