Commit 9d097088 authored by Jean Mainguy's avatar Jean Mainguy
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Update usage.md for hifi assembly

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**WARNING 3:** `S02_ASSEMBLY` step depends on `S01_CLEAN_QC` step. You need to use the mandatory files of these two steps to run `S02_ASSEMBLY`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md#ii-input-files) and **WARNINGS 1 and 2**.
* `--assembly ["metaspades" or "megahit"]`: allows to indicate the assembly tool. Default: `metaspades`.
* `--assembly` allows to indicate the assembly tool. For short reads: `["metaspades" or "megahit"]`: Default: `metaspades`.
For HiFi reads: `["hifiasm-meta", "metaflye"]`. Default: `hifiasm-meta`.
**WARNING 4:** For short reads, the user can choose between `metaspades` or `megahit` for `--assembly` parameter. The choice can be based on CPUs and memory availability: `metaspades` needs more CPUs and memory than `megahit` but our tests showed that assembly metrics are better for `metaspades` than `megahit`.For PacBio HiFi reads, the user can choose between `hifiasm-meta` or `metaflye`.
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