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In Print: Last Week's Sequencing-Related Papers of Note: Jan 8, 2013


Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing.
Michaeli M, Noga H, Tabibian-Keissar H, Barshack I, Mehr R.
Front Immunol. 2012;3:386.

Identifying RNA editing sites using RNA sequencing data alone.
Ramaswami G, Zhang R, Piskol R, Keegan LP, et al.
Nat Methods. 2013 Jan 6. [Epub ahead of print]

ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES, Li B, Li C.
BMC Res Notes. 2013 Jan 4;6(1):5.

Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing.
Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G.
Nat Protoc. 2013 Jan 3;8(1):176-89.

HTS-PEG: A method for high throughput sequencing of the paired-ends of genomic libraries.
Zhou S, Fu Y, Li J, He L, et al.
PLoS One. 2012;7(12):e52257.

Palindromic nucleotide analysis in human T cell receptor rearrangements.
Srivastava SK, Robins HS.
PLoS One. 2012;7(12):e52250.

FastUniq: A fast de novo duplicates removal tool for paired short reads.
Xu H, Luo X, Qian J, Pang X, et al.
PLoS One. 2012;7(12):e52249.

Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons.
Vezzi F, Narzisi G, Mishra B.
PLoS One. 2012;7(12):e52210.

Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
Tang S, Gong Y, Edwards EA.
PLoS One. 2012;7(12):e52038.

Microbial analysis of bite marks by sequence comparison of streptococcal DNA.
Kennedy DM, Stanton JA, García JA, Mason C, et al.
PLoS One. 2012;7(12):e51757.

Estimation of copy number alterations from exome sequencing data.
Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS.
PLoS One. 2012;7(12):e51422.

Studying DNA translocation in nanocapillaries using single molecule fluorescence.
Thacker VV, Ghosal S, Hernández-Ainsa S, Bell NA, Keyser UF.
Appl Phys Lett. 2012 Nov 26;101(22):223704.

Sequencing of isolated sperm cells for direct haplotyping of a human genome.
Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, et al.
Genome Res. 2013 Jan 2. [Epub ahead of print]
(See our coverage of this paper in this issue here.)

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.).
Allen AM, Barker GL, Wilkinson P, Burridge A, et al.
Plant Biotechnol J. 2012 Dec 20. [Epub ahead of print]

Genomic region operation kit for flexible processing of deep sequencing data.
Ovaska K, Lyly L, Sahu B, Janne OA, Hautaniemi S.
IEEE/ACM Trans Comput Biol Bioinform. 2012 Dec 28. [Epub ahead of print]

NucBase, an easy to use read mapper for small RNAs.
Dufourt J, Pouchin P, Peyret P, Brasset E, Vaury C.
Mob DNA. 2013 Jan 1;4(1):1.