a-ludi
commented
3 years ago Hi,
yes, dentist.json is the place. You can place them all under __default__ which means that they apply to every stage. Please remove the leading dashes (--), e.g.:
{
"__default__": {
"max-insertion-error": 0.15,
"min-anchor-length": 1500,
"min-reads-per-pile-up": 1,
"min-spanning-reads": 1,
"allow-single-reads": true,
"join-policy": "contigs"
}
}It seems like you want to create a more greedy configuration. Please be aware that you should not further reduce min-anchor-length as it is already rather sensitive to repeat masking errors – it may even lead to reduced number of closed gaps because more scaffolding conflicts appear. Finally, here is an example for a greedy configuration I am intending to put into the next release:
{
"// WARNING": [
"Use with care!",
"Always validate the closed gaps (e.g. manual inspection)."
],
"// NOTE": [
"The workflow creates an intermediate assembly",
"`workdir/{output_assembly}-preliminary.fasta` that contains all",
"closed gaps, i.e. before validation. It is accompanied by an AGP",
"and BED file. You may inspect these file for maximum sensitivity."
],
"__default__": {
"verbose": 2,
"agp": "true",
"allow-single-reads": true,
"best-pile-up-margin": 1.5,
"existing-gap-bonus": 3.0,
"join-policy": "contigs",
"min-reads-per-pile-up": 1,
"min-spanning-reads": 1,
"proper-alignment-allowance": 500
},
"// Uncomment the following block if": [
"the default value for min-coverage-reads",
"(0.5 * --read-coverage/--ploidy) is suboptimal. It is important to",
"revert --read-coverage and --ploidy because they are mutually exclusive",
"with --min-coverage-reads."
]
}
oushujun
When setting the parameters below, do these need to be included in the dentist.json config file? and if so in which section?
--max-insertion-error --min-anchor-length --min-reads-per-pile-up --min-spanning-reads --allow-single-reads --join-policy