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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Request to optionally remove --careful flag from spades reassembly #367

Open franciscozorrilla opened 3 years ago

franciscozorrilla commented 3 years ago

For very large metagenomes (~30 Gb size, 400 M reads) the spades reassembly can get bottlenecked during error/mismatch correction for hours. Removing the --careful flag from the spades call fixed the problem, and also resulted in bins with better completeness and contamination (relative to input bins).

ursky commented 3 years ago

This is great to know, thank you. I will eventually add this as a feature, but in the meantime the easiest thing to do on the user side would be to just go into proxiwrap_modules/assembly.sh and removing the flag manually.