Workflows and e-Science: An overview of workflow system features and capabilities
Future Generation Computer Systems
Bioinformatics
Bioinformatics
High-Throughput Compression of FASTQ Data with SeqDB
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We present a new Python/C++ framework, BioLite, for implementing bioinformatics pipelines for Next-Generation Sequencing (NGS) data. BioLite tracks provenance of analyses, automates the collection and reporting of diagnostics (such as summary statistics and plots at intermediate stages), and profiles computational requirements. These diagnostics can be accessed across multiple stages of a pipeline, from other pipelines, and in HTML reports. Finally, we describe several use cases for diagnostics in our own analyses.