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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.

The Scan

Call to Look Again

More than a dozen researchers penned a letter in Science saying a previous investigation into the origin of SARS-CoV-2 did not give theories equal consideration.

Not Always Trusted

In a new poll, slightly more than half of US adults have a great deal or quite a lot of trust in the Centers for Disease Control and Prevention, the Hill reports.

Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.