diff --git a/docs/index.md b/docs/index.md index e73218e8..2f33cf91 100644 --- a/docs/index.md +++ b/docs/index.md @@ -122,7 +122,7 @@ usage: ganon [-h] [-v] - - - - - - - - - - _ _ _ _ _ (_|(_|| |(_)| | - _| v. 1.7.0 + _| v. 1.8.0 - - - - - - - - - - positional arguments: @@ -146,9 +146,9 @@ options: ganon build ``` -usage: ganon build [-h] [-g [...]] [-a [...]] [-b [...]] [-o] [-c] [-r] [-u] [-m [...]] [-z [...]] [--skip-genome-size] - -d DB_PREFIX [-x] [-t] [-p] [-f] [-k] [-w] [-s] [-j] [-y] [--hibf] [--restart] [--verbose] [--quiet] - [--write-info-file] +usage: ganon build [-h] [-g [...]] [-a [...]] [-l] [-b [...]] [-o] [-c] [-r] [-u] [-m [...]] [-z [...]] + [--skip-genome-size] -d DB_PREFIX [-x] [-t] [-p] [-f] [-k] [-w] [-s] [-j] [-y] [--hibf] [--restart] + [--verbose] [--quiet] [--write-info-file] options: -h, --help show this help message and exit @@ -164,6 +164,10 @@ required arguments: -d DB_PREFIX, --db-prefix DB_PREFIX Database output prefix (default: None) +database arguments: + -l , --level Highest level to build the database. Options: any available taxonomic rank [species, genus, + ...], 'leaves' or 'assembly' (default: assembly) + download arguments: -b [ ...], --source [ ...] Source to download [refseq, genbank] (default: ['refseq']) @@ -187,7 +191,8 @@ important arguments: -t , --threads advanced arguments: - -p , --max-fp Max. false positive rate for bloom filters Mutually exclusive --filter-size. (default: 0.05) + -p , --max-fp Max. false positive for bloom filters. Mutually exclusive --filter-size. Defaults to 0.05 or + 0.001 with --hibf. (default: None) -f , --filter-size Fixed size for filter in Megabytes (MB). Mutually exclusive --max-fp. (default: 0) -k , --kmer-size The k-mer size to split sequences. (default: 19) -w , --window-size The window-size to build filter with minimizers. (default: 31) @@ -200,7 +205,7 @@ advanced arguments: to balance classification speed and database size. (default: avg) -y , --min-length Skip sequences smaller then value defined. 0 to not skip any sequence. (default: 0) --hibf Builds an HIBF with raptor/chopper (v3). --mode, --filter-size and --min-length will be ignored. - (default: False) + This option will set --max-fp 0.001 as default. (default: False) optional arguments: --restart Restart build/update from scratch, do not try to resume from the latest possible step. @@ -273,7 +278,8 @@ important arguments: -t , --threads advanced arguments: - -p , --max-fp Max. false positive rate for bloom filters Mutually exclusive --filter-size. (default: 0.05) + -p , --max-fp Max. false positive for bloom filters. Mutually exclusive --filter-size. Defaults to 0.05 or + 0.001 with --hibf. (default: None) -f , --filter-size Fixed size for filter in Megabytes (MB). Mutually exclusive --max-fp. (default: 0) -k , --kmer-size The k-mer size to split sequences. (default: 19) -w , --window-size The window-size to build filter with minimizers. (default: 31) @@ -286,7 +292,7 @@ advanced arguments: to balance classification speed and database size. (default: avg) -y , --min-length Skip sequences smaller then value defined. 0 to not skip any sequence. (default: 0) --hibf Builds an HIBF with raptor/chopper (v3). --mode, --filter-size and --min-length will be ignored. - (default: False) + This option will set --max-fp 0.001 as default. (default: False) optional arguments: --restart Restart build/update from scratch, do not try to resume from the latest possible step.