Literature DB >> 21278192

SHRiMP2: sensitive yet practical SHort Read Mapping.

Matei David1, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno.   

Abstract

UNLABELLED: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures. AVAILABILITY: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.

Mesh：

Year:  2011        PMID： 21278192     DOI： 10.1093/bioinformatics/btr046

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  172 in total

1.  Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Authors:  Sophie Schbath; Véronique Martin; Matthias Zytnicki; Julien Fayolle; Valentin Loux; Jean-François Gibrat
Journal:  J Comput Biol       Date:  2012-04-16       Impact factor: 1.479

2.  Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.

Authors:  Scott A Beatson; Nouri L Ben Zakour; Makrina Totsika; Brian M Forde; Rebecca E Watts; Amanda N Mabbett; Jan M Szubert; Sohinee Sarkar; Minh-Duy Phan; Kate M Peters; Nicola K Petty; Nabil-Fareed Alikhan; Mitchell J Sullivan; Jayde A Gawthorne; Mitchell Stanton-Cook; Nguyen Thi Khanh Nhu; Teik Min Chong; Wai-Fong Yin; Kok-Gan Chan; Viktoria Hancock; David W Ussery; Glen C Ulett; Mark A Schembri
Journal:  Infect Immun       Date:  2015-02-09       Impact factor: 3.441

3.  Exacerbated Staphylococcus aureus Foot Infections in Obese/Diabetic Mice Are Associated with Impaired Germinal Center Reactions, Ig Class Switching, and Humoral Immunity.

Authors:  Christopher W Farnsworth; Eric M Schott; Abigail Benvie; Stephen L Kates; Edward M Schwarz; Steven R Gill; Michael J Zuscik; Robert A Mooney
Journal:  J Immunol       Date:  2018-06-01       Impact factor: 5.422

4.  Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation.

Authors:  Jeffrey Malik; Michael Getman; Laurie A Steiner
Journal:  Mol Cell Biol       Date:  2015-04-06       Impact factor: 4.272

5.  Direct regulation of diurnal Drd3 expression and cocaine reward by NPAS2.

Authors:  Angela R Ozburn; Edgardo Falcon; Alan Twaddle; Alexandria L Nugent; Andrea G Gillman; Sade M Spencer; Rachel N Arey; Shibani Mukherjee; James Lyons-Weiler; David W Self; Colleen A McClung
Journal:  Biol Psychiatry       Date:  2014-08-13       Impact factor: 13.382

Review 6.  Review of alignment and SNP calling algorithms for next-generation sequencing data.

Authors:  M Mielczarek; J Szyda
Journal:  J Appl Genet       Date:  2015-06-09       Impact factor: 3.240

7.  The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

Authors:  Estienne C Swart; John R Bracht; Vincent Magrini; Patrick Minx; Xiao Chen; Yi Zhou; Jaspreet S Khurana; Aaron D Goldman; Mariusz Nowacki; Klaas Schotanus; Seolkyoung Jung; Robert S Fulton; Amy Ly; Sean McGrath; Kevin Haub; Jessica L Wiggins; Donna Storton; John C Matese; Lance Parsons; Wei-Jen Chang; Michael S Bowen; Nicholas A Stover; Thomas A Jones; Sean R Eddy; Glenn A Herrick; Thomas G Doak; Richard K Wilson; Elaine R Mardis; Laura F Landweber
Journal:  PLoS Biol       Date:  2013-01-29       Impact factor: 8.029

8.  The lipoprotein LpqW is essential for the mannosylation of periplasmic glycolipids in Corynebacteria.

Authors:  Arek K Rainczuk; Yoshiki Yamaryo-Botte; Rajini Brammananth; Timothy P Stinear; Torsten Seemann; Ross L Coppel; Malcolm J McConville; Paul K Crellin
Journal:  J Biol Chem       Date:  2012-10-22       Impact factor: 5.157

9.  pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence.

Authors:  Eva C Boritsch; Wafa Frigui; Alessandro Cascioferro; Wladimir Malaga; Gilles Etienne; Françoise Laval; Alexandre Pawlik; Fabien Le Chevalier; Mickael Orgeur; Laurence Ma; Christiane Bouchier; Timothy P Stinear; Philip Supply; Laleh Majlessi; Mamadou Daffé; Christophe Guilhot; Roland Brosch
Journal:  Nat Microbiol       Date:  2016-01-27       Impact factor: 17.745

10.  Identification of a homozygous splice site mutation in the dynein axonemal light chain 4 gene on 22q13.1 in a large consanguineous family from Pakistan with congenital mirror movement disorder.

Authors:  Iltaf Ahmed; Kirti Mittal; Taimoor I Sheikh; Nasim Vasli; Muhammad Arshad Rafiq; Anna Mikhailov; Mehrnaz Ohadi; Huda Mahmood; Guy A Rouleau; Attya Bhatti; Muhammad Ayub; Myriam Srour; Peter John; John B Vincent
Journal:  Hum Genet       Date:  2014-08-07       Impact factor: 4.132
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