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LiaOb21 committed Apr 29, 2024
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42 changes: 40 additions & 2 deletions config/README.md
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@@ -254,7 +254,45 @@ You can optionally give as input the reference genome for the species under stud

All the parameters that you can customise for quast are optional, and you can refer to [quast documentation](https://quast.sourceforge.net/docs/manual.html) to see which ones are suitable for your case.

### 1. Example
### 2. Example
### 1. Example running quast with no reference genome

In this case just leave all the optional parameters empty:
```
# Customisable parameters for quast
quast:
optional_params:
"--fragmented": ""
"--large": ""
```

### 2. Example running quast with reference genome

In this case you have to previously download your reference genome (and GFF, if you want), and specify the path with the `-r` flag (`-g` for the GFF):
```
# Customisable parameters for quast
quast:
optional_params:
"--fragmented": ""
"--large": ""
"-r": "resources/reference_genomes/yeast/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa"
"-g": "resources/reference_genomes/yeast/Saccharomyces_cerevisiae.R64-1-1.101.gff3"
```

# Busco

Busco is used to perform the quality check of the assembly along all the workflow. It processes:

- contig level assembly(ies) produced by hifiasm
- decontaminated contig level assembly(ies) produced by fcs-gx (if included)
- purged contig level primary assembly produced by purge_dups (if included)
- scaffolded assembly(ies) produced by yahs

You must download the busco lineage of your interest before running colora. See [here](https://github.com/LiaOb21/colora/tree/main?tab=readme-ov-file#snakemake-workflow-colora) for instructions on how to download the busco lineage.

You need to specify the path to your busco lineage in the config file:

```
# Customisable parameters for busco
busco:
lineage: "resources/saccharomycetes_odb10" # lineage to be used for busco analysis
```

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