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Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation.
Georgiy Golovko1, Kamil Khanipov, Mark Rojas
1Center for BioMedical and Environmental Genomics, University of Houston, Houston, TX, USA. ggolovko@bioinfo.uh.edu
BMC Bioinformatics
|July 18, 2012
Summary
Slim-Filter is a Windows application for analyzing Next-Generation Sequencing (NGS) data. It simplifies tasks like read filtration and quality assessment for individual researchers, reducing reliance on bioinformatics services.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Next-Generation Sequencing (NGS) generates massive datasets, posing challenges for individual researchers.
- Large file sizes limit effective data analysis and manipulation, requiring multi-step processes.
- Reliance on bioinformatics services can be problematic and requires specialized computational facilities.
Purpose of the Study:
- To present Slim-Filter, a Windows-based application for interactive analysis of sequencing reads.
- To provide individual investigators with integrated capabilities for sequencing data manipulation and curation.
- To streamline common NGS data processing tasks.
Main Methods:
- Developed a Windows-based application (Slim-Filter) using C++.
- Implemented interactive examination of sequencing read statistical properties.
- Included functionalities for read filtration (quality, complexity, subsequences, duplicates) and sorting.
- Supported fasta, fastq, and specialized AS file formats.
Main Results:
- Slim-Filter enables interactive quality assessment and filtration of low-quality/complexity reads.
- The application filters reads containing adapter or primer sequences and removes duplicates.
- It allows sorting reads by copy number, facilitating manual editing and analysis.
- Features include a sequential window interface and roll-back capabilities for data manipulation steps.
Conclusions:
- Slim-Filter empowers individual researchers with integrated tools for sequencing read analysis.
- The application simplifies complex data manipulation tasks, enhancing accessibility.
- It addresses the need for efficient and user-friendly NGS data processing solutions.
