The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

Li, Jing‐Woei; Robison, Keith; Martin, Marcel; Sjödin, Andreas; Usadel, Björn; Young, Matthew; Olivares, Eric C.; Bolser, Dan

doi:10.1093/nar/gkr1058

Cited by 35 publications

(24 citation statements)

References 8 publications

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“…For example, one of the tools repositories that has been integrated into the Bio-TDS is SEQAnswer-Wiki SEQ, the most relevant tools repository for the High Throughput Sequencing (HTS) community (e.g. NGS, RNASeq, ChipSeq) (4,12). …”

Section: Introductionmentioning

confidence: 99%

Bio-TDS: bioscience query tool discovery system

et al. 2016

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Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 15 000 analytic tool descriptions integrated from well-established, community repositories. One of the primary components of the Bio-TDS is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS’s scientific impact was evaluated using sample questions posed by researchers retrieved from Biostars, a site focusing on biological data analysis. The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness. The Bio-TDS offers researchers the capacity to associate their bioscience question with the most relevant computational toolsets required for the data analysis in their knowledge discovery process.

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Section: Introductionmentioning

confidence: 99%

Bio-TDS: bioscience query tool discovery system

et al. 2016

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“…The majority of these directories focus either on software tools or databases and on a particular application (13). OMICtools differs in scope.…”

Section: Discussionmentioning

confidence: 99%

OMICtools: an informative directory for multi-omic data analysis

Henry¹,

Bandrowski²,

Pépin³

et al. 2014

Database

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Recent advances in ‘omic’ technologies have created unprecedented opportunities for biological research, but current software and database resources are extremely fragmented. OMICtools is a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics and metabolomics. All tools have been classified by omic technologies (next-generation sequencing, microarray, mass spectrometry and nuclear magnetic resonance) associated with published evaluations of tool performance. Information about each tool is derived either from a diverse set of developers, the scientific literature or from spontaneous submissions. OMICtools is expected to serve as a useful didactic resource not only for bioinformaticians but also for experimental researchers and clinicians.Database URL: http://omictools.com/

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“…Adapter parts might be erroneously sequenced in the beginning of a read, and thus may introduce artificial mutations [35][36][37]. There are a number of popular tools for adaptor removing from raw sequence reads [34,[38][39][40].…”

Section: Box 3: Base Calls Their Qualities and Readsmentioning

confidence: 99%