Value, but high costs in post-deposition data curation

Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Value, but high costs in post-deposition data Curation

© The Author(s) 2016. Published by Oxford University Press. Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

A novel and well-defined benchmarking method for second generation read mapping

Background Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. Results We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. Conclusions We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan.de/projects/rabema.html

Ten-year audit of Lichtenstein hernioplasty under local anaesthesia performed by surgical residents

<p>Abstract</p> <p>Background</p> <p>To analyse in a prospective trial the long-term results of Lichtenstein hernioplasty performed by surgical trainees.</p> <p>Methods</p> <p>Training of tension-free Lichtenstein hernia operation was started in our ambulatory unit as an outpatient procedure under local anaesthesia in 1996. After performing 36 teaching operations together with residents and their supervising specialist, 281 patients were operated during 1996-2000 either by one senior consultant (n = 141) or by 12 surgical trainees (n = 140). After 10 years, 247 (88%) patients were available for the long-term assessment.</p> <p>Results</p> <p>After one month postoperatively, the rate of wound infections (consultant 1.1%, residents 0.7%) and hematomas (consultant 1.1%, residents 3.0%) were low and not related to surgeon's training level (ns). Only 6 (2.1%) clinically evident recurrences were found after 10 years: two after specialist repair and four after trainee repair (ns). Although one third of the patients reported some discomfort after 3 and 10 years, 93-95% of the patients were very satisfied with the operation, with no statistical difference between the surgeons.</p> <p>Conclusion</p> <p>Ambulatory open mesh repair under local anaesthesia was a safe operation and the long-term results were acceptable among the patients operated by surgical trainees.</p