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Recent Sequencing-Related Papers of Note: Jun 24, 2014

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The "Grep" command but not FusionMap, FusionFinder or ChimeraScan captures the CIC-DUX4 fusion gene from whole transcriptome sequencing data on a small round cell tumor with t(4;19)(q35;q13).
Panagopoulos I, Gorunova L, Bjerkehagen B, Heim S.
PLOS One. 2014 Jun 20;9(6):e99439.


BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.
Luo R, Wong YL, Law WC, Lee LK, et al.
PeerJ. 2014 Jun 3;2:e421.


A novel multi-alignment pipeline for high-throughput sequencing data.
Huang S, Holt J, Kao CY, McMillan L, Wang W.
Database (Oxford). 2014 Jun 18;2014.


Omega: an overlap-graph de novo assembler for metagenomics.
Haider B, Ahn TH, Bushnell B, Chai J, et al.
Bioinformatics. 2014 Jun 19. [Epub ahead of print]


Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum.
Evans J, Kim J, Childs KL, Vaillancourt B, et al.
Plant J. 2014 Jun 20. [Epub ahead of print]


Whole genome analysis of Exserohilum rostratum from the outbreak of fungal meningitis and other infections.
Litvintseva AP, Hurst S, Gade L, Frace MA, et al.
J Clin Microbiol. 2014 Jun 20. [Epub ahead of print]


SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.
Boetzer M, Pirovano W.
BMC Bioinformatics. 2014 Jun 20;15(1):211.


BEETL-fastq: a searchable compressed archive for DNA reads.
Janin L, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2014 Jun 20. [Epub ahead of print]


Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.
Jiang P, Sun K, Lun FM, Guo AM, et al.
PLOS One. 2014 Jun 19;9(6):e100360.


Choice of transcripts and software has a large effect on variant annotation.
McCarthy DJ, Humburg P, Kanapin A, Rivas MA, et al.
Genome Med. 2014 Mar 31;6(3):26.


Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms.
Nassirpour R, Mathur S, Gosink MM, Li Y, et al.
BMC Genomics. 2014 Jun 18;15(1):485.


Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the iceman.
Maixner F, Thomma A, Cipollini G, Widder S, et al.
PLOS One. 2014 Jun 18;9(6):e99994.


Standards for sequencing viral genomes in the era of high-throughput sequencing.
Ladner JT, Beitzel B, Chain PS, Davenport MG, et al.
MBio. 2014 Jun 17;5(3).


FGAP: an automated gap closing tool.
Piro VC, Faoro H, Weiss VA, Steffens MB, et al.
BMC Res Notes. 2014 Jun 18;7(1):371.


CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.
Naquin D, D Aubenton-Carafa Y, Thermes C, Silvain M.
BMC Bioinformatics. 2014 Jun 18;15(1):198.


Mapping breakpoints of a familial chromosome insertion (18:7) (q22.1; q36.2q21.11) to DPP6 and CACNA2D1 genes in an azoospermic male.
Li L, Chen H, Yin C, Yang C, et al.
Gene. 2014 Jun 14. [Epub ahead of print]


Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.
Kim HK, Park WC, Lee KM, Hwang HL, et al.
PLOS One. 2014 Jun 17;9(6):e100089.


Standardized metadata for human pathogen/vector genomic sequences.
Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, et al.
PLOS One. 2014 Jun 17;9(6):e99979.


OccuPeak: ChIP-seq peak calling based on internal background modelling.
de Boer BA, van Duijvenboden K, van den Boogaard M, Christoffels VM, et al.
PLOS One. 2014 Jun 17;9(6):e99844.


Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.
Monden Y, Yamamoto A, Shindo A, Tahara M.
DNA Res. 2014 Jun 16. [Epub ahead of print]


Hydrodynamic slip on DNA observed by optical tweezers-controlled translocation experiments with solid-state and lipid-coated nanopores.
Galla L, Meyer AJ, Spiering A, Sischka A, et al.
Nano Lett. 2014 Jun 17. [Epub ahead of print]


Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers.
Cao CC, Li C, Sun X.
BMC Bioinformatics. 2014 Jun 17;15(1):195.


A pressure-voltage trap for DNA near a solid-state nanopore.
Hoogerheide DP, Lu B, Golovchenko JA.
ACS Nano. 2014 Jun 16. [Epub ahead of print]


Stiff filamentous virus translocations through solid-state nanopores.
McMullen A, de Haan HW, Tang JX, Stein D.
Nat Commun. 2014 Jun 16;5:4171.


Accurate viral population assembly from ultra-deep sequencing data.
Mangul S, Wu NC, Mancuso N, Zelikovsky A, et al.
Bioinformatics. 2014 Jun 15;30(12):i329-i337.


AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
Bao E, Jiang T, Girke T.
Bioinformatics. 2014 Jun 15;30(12):i319-i328.


Ragout-a reference-assisted assembly tool for bacterial genomes.
Kolmogorov M, Raney B, Paten B, Pham S.
Bioinformatics. 2014 Jun 15;30(12):i302-i309.


ExSPAnder: a universal repeat resolver for DNA fragment assembly.
Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, et al.
Bioinformatics. 2014 Jun 15;30(12):i293-i301.


RNA-Skim: a rapid method for RNA-seq quantification at transcript level.
Zhang Z, Wang W.
Bioinformatics. 2014 Jun 15;30(12):i283-i292.


Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.
Rampášek L, Arbabi A, Brudno M.
Bioinformatics. 2014 Jun 15;30(12):i212-i218.


Privacy preserving protocol for detecting genetic relatives using rare variants.
Hormozdiari F, Joo JW, Wadia A, Guan F, et al.
Bioinformatics. 2014 Jun 15;30(12):i204-i211.


Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.
Aijö T, Butty V, Chen Z, Salo V, et al.
Bioinformatics. 2014 Jun 15;30(12):i113-i120.


Analysis by high throughput sequencing of specific pathogen free eggs.
Gagnieur L, Cheval J, Cochet M, Breard E, et al.
Biologicals. 2014 Jun 12. [Epub ahead of print]

The Scan

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Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

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The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.