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A review of software for analyzing molecular sequences
Haema Nilakanta, Kimberly L Drews, Suzanne Firrell
1The Biostatistics Center, The George Washington University, 6110 Executive Boulevard 750, Rockville, MD 20852-3943, USA. kjablons@gwu.edu.
BMC Research Notes
|November 26, 2014
Summary
Choosing microbiome analysis software can be difficult. This review compares seven free packages for microbial sequence analysis, highlighting mothur and QIIME for their comprehensive features and documentation.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- Microbiome research has rapidly expanded over the last decade.
- Numerous software packages exist for analyzing microbial community sequences (e.g., 16S rRNA gene).
- Selecting appropriate analysis software is challenging for new researchers.
Purpose of the Study:
- To systematically review available software packages for microbial sequence analysis.
- To provide guidance for students and researchers in choosing the best analytical pipeline.
- To offer the first comprehensive review of such software.
Main Methods:
- Conducted a systematic review of publicly available, cost-free software.
- Included packages offering end-to-end analysis from sequencing to results presentation.
- Ensured selected packages had documentation and data security.
Main Results:
- Seven software packages met the inclusion criteria.
- Each package's installation, documentation, features, and functions were described.
- Installation and execution of each software package were performed.
Conclusions:
- Software availability may be limited by operating system compatibility.
- Users must understand each package's features, functions, default settings, and assumptions.
- While all packages have limitations in longitudinal analysis, mothur and QIIME are recommended for their comprehensive features and documentation.
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