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Hydro3639 / NanoPhase

Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)
MIT License
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Add flag for nano-raw #11

Open joao1980 opened 3 months ago

joao1980 commented 3 months ago

Hi, is it possible to modify the tool to allow users to change the flag of flyes' nano-hq to nano-raw? Thanks, Joao

Hydro3639 commented 3 months ago

Hi Joao,

Nanophase-generated MAGs are based on long-read assembly, followed by binning and long-read polishing (or short-read polishing if you have). To achieve high-quality/accuracy or complete genome reconstruction, it's recommended that you use long reads generated from Q20+ chemistry. These reads offer superior sequencing accuracy, which is crucial for avoiding INDEL errors. That's why the default assembly setting for flye is 'nano-hq'. However, if you're using ONT reads with high sequencing error and choose to use 'nano-raw', it's unclear how well Nanophase will perform. If you're working with high error-prone ONT reads, you may want to consider a short-read-first approach if short reads are available in your study.

So, currently, sorry that I don't have a plan to add "nano-raw" in nanophase. However, if you really want to try 'nano-raw', the easiest way is to change the relevant commands directly. For example, if you are using 'nanophase meta', the flye-assembly command is in line 217 in the nanophase.meta script: change --nano-hq to nano-raw. Let me know if you need more help.

Best regards