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Welcome to the MEGAHIT wiki!

FAQ

Q: How to set memory usage for MEGAHIT?

A: Since version 0.3.0, MEGAHIT will set the memory for its sdbg_builder automatically. For manual setting, please refer to this page.

Q: Can MEGAHIT support pair-end reads?

A: Yes since version 0.3.0. In previous version PE reads are taken by MEGAHIT as Single-ended.

Q: How to use --input-cmd option?

A: Please refer to this page. However, basically --input-cmd is not recommended since version 0.3.0, because all reads input in this way are taken as single-ended.

Q: Is it possible to visualize MEGAHIT's assembly graph?

A: Yes. Please refer to Visualizing-MEGAHIT's-contig-graph.

Q: How to solve the problem of "Error occurs when assembling contigs for k=xxx [Exit code -4]"?

A: Recompile MEGAHIT by make clean && make disablempopcnt=1.

Q: There are many files in the folder "intermediate_contigs", what are they?

A: See this post.

Assembly Tips

https://github.com/voutcn/megahit/wiki/Assembly-Tips