Dataset Information

SATRAP: SOLiD Assembler TRAnslation Program.

ABSTRACT: SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing totally wrong results. Here we describe SATRAP, a computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format. The program was tested and validated using simulated and real transcriptomic data; its modularity allows an easy integration into more complex pipelines, such as Oases for RNA-seq de novo assembly. SATRAP is available at http://satrap.cribi.unipd.it, either as a multi-step pipeline incorporating several tools for RNA-seq assembly or as an individual module for use with the Oases package.

SUBMITTER: Campagna D

PROVIDER: S-EPMC4569514 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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SATRAP: SOLiD Assembler TRAnslation Program.

Campagna Davide D Gasparini Fabio F Franchi Nicola N Manni Lucia L Telatin Andrea A Vitulo Nicola N Ballarin Loriano L Valle Giorgio G

PloS one 20150914 9

SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing totally wrong results. Here we describe SATRAP, a computer program designed to efficiently translate de n ...[more]

PMID: 26368549

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Project description:INTRODUCTION:This clinical demonstration trial compared the effectiveness of the Veterans Affairs Diabetes Prevention Program (VA-DPP) with an evidence-based usual care weight management program (MOVE!®) in the Veterans Health Administration health system. DESIGN:Prospective, pragmatic, non-randomized comparative effectiveness study of two behavioral weight management interventions. SETTING/PARTICIPANTS:Obese/overweight Veterans with prediabetes were recruited from three geographically diverse VA sites between 2012 and 2014. INTERVENTION:VA-DPP included 22 group-based intensive lifestyle change sessions. MAIN OUTCOME MEASURES:Weight change at 6 and 12 months, hemoglobin A1c (HbA1c) at 12 months, and VA health expenditure changes at 15 months were assessed using VA electronic health record and claims data. Between- and within-group comparisons for weight and HbA1c were done using linear mixed-effects models controlling for age, gender, race/ethnicity, baseline outcome values, and site. Analyses were conducted in 2015-2016. RESULTS:A total of 387 participants enrolled (273 VA-DPP, 114 MOVE!). More VA-DPP participants completed at least one (73.3% VA-DPP vs 57.5% MOVE! p=0.002); four (57.5% VA-DPP vs 42.5% MOVE!, p=0.007); and eight or more sessions (42.5% VA-DPP vs 31% MOVE!, p=0.035). Weight loss from baseline was significant at both 6 (p<0.001) and 12 months (p<0.001) for VA-DPP participants, but only significant at 6 months for MOVE! participants (p=0.004). Between groups, there were significant differences in 6-month weight loss (-4.1 kg VA-DPP vs -1.9 kg MOVE!, p<0.001), but not 12-month weight loss (-3.4 kg VA-DPP vs -2.0 kg MOVE!, p=0.16). There were no significant differences in HbA1c change or outpatient, inpatient, and total VA expenditures. CONCLUSIONS:VA-DPP participants had higher participation rates and weight loss at 6 months, but similar weight, HbA1c, and health expenditures at 12 months compared to MOVE! PARTICIPANTS:Features of VA-DPP may help enhance the capability of MOVE! to reach a larger proportion of the served population and promote individual-level weight maintenance.

Dataset Information

SATRAP: SOLiD Assembler TRAnslation Program.

Publications

SATRAP: SOLiD Assembler TRAnslation Program.

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