Frequently Asked Questions
This document is under development. Common questions will be added based on user feedback.
Table of Contents
- Installation and Setup
- Assembly Questions
- Performance and Optimization
- Data Formats and Compatibility
- Error Messages and Troubleshooting
- Comparison with Other Tools
Installation and Setup
Q: What are the system requirements for Mycelia?
TODO: Add system requirements FAQ
Q: How do I install Mycelia on my HPC cluster?
TODO: Add HPC installation FAQ
Q: Can I use Mycelia with conda environments?
TODO: Add conda integration FAQ
Assembly Questions
Q: Which assembly method should I use for my data?
TODO: Add method selection FAQ - reference assembly-method-selection.md
Q: How do I choose the right k-mer size?
TODO: Add k-mer selection FAQ
Q: What does "probabilistic assembly" mean?
TODO: Add probabilistic assembly explanation
Q: How is Mycelia different from SPAdes or other assemblers?
TODO: Add comparison FAQ
Performance and Optimization
Q: How much memory do I need for my genome size?
TODO: Add memory estimation FAQ - reference performance.md
Q: My assembly is taking too long. How can I speed it up?
TODO: Add performance optimization FAQ
Q: Can I run Mycelia in parallel?
TODO: Add parallelization FAQ
Data Formats and Compatibility
Q: What file formats does Mycelia support?
TODO: Add file format FAQ
Q: Can I use compressed FASTQ files?
TODO: Add compression support FAQ
Q: How do I convert between different sequence formats?
TODO: Add format conversion FAQ
Error Messages and Troubleshooting
Q: I'm getting "OutOfMemoryError" - what should I do?
TODO: Add memory error troubleshooting
Q: The assembly produced no contigs. What went wrong?
TODO: Add empty assembly troubleshooting
Q: How do I interpret assembly quality metrics?
TODO: Add quality interpretation FAQ
Comparison with Other Tools
Q: When should I use Mycelia vs SPAdes?
TODO: Add SPAdes comparison
Q: How does Mycelia compare to Flye for long reads?
TODO: Add Flye comparison
Q: Can I use Mycelia results with downstream tools?
TODO: Add compatibility FAQ
Getting Help
Q: Where can I get help if my question isn't answered here?
TODO: Add help resources
- GitHub Issues for bug reports
- GitHub Discussions for questions
- Documentation and tutorials
Q: How do I report a bug or request a feature?
TODO: Add bug reporting guidance
Q: Is there a community forum or chat?
TODO: Add community resources
This FAQ will be expanded based on common user questions and issues. If you have a question not covered here, please ask in GitHub Discussions.