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update docs
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gtonkinhill committed Oct 7, 2024
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36 changes: 30 additions & 6 deletions docs/gettingstarted/params.md
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Expand Up @@ -15,6 +15,8 @@ Thus to align all genes present in at least 98% of isolates using clustal and 10
panaroo -i *.gff -o ./results/ --clean-mode strict -a core --aligner clustal --core_threshold 0.98 -t 10
```

You can also output unaligned gene sequences by specifying `--aligner none`. Additionally, user @revinci has provided a separate script for generating alignments after running Panaroo, which is described [here](https://github.com/gtonkinhill/panaroo/issues/306).

#### Cluster Thresholds

The Panaroo algorithm initially performs a conservative clustering step before collapsing genes into possible families. It is usually best to use the dafault parameters for this initial clustering stage.
Expand Down Expand Up @@ -54,9 +56,11 @@ panaroo -i *.gff -o ./results/ --clean-mode strict --refind_prop_match 0.5 --sea
usage: panaroo [-h] -i INPUT_FILES [INPUT_FILES ...] -o OUTPUT_DIR
--clean-mode {strict,moderate,sensitive}
[--remove-invalid-genes] [-c ID] [-f FAMILY_THRESHOLD]
[--len_dif_percent LEN_DIF_PERCENT] [--merge_paralogs]
[--search_radius SEARCH_RADIUS]
[--len_dif_percent LEN_DIF_PERCENT]
[--family_len_dif_percent FAMILY_LEN_DIF_PERCENT]
[--merge_paralogs] [--search_radius SEARCH_RADIUS]
[--refind_prop_match REFIND_PROP_MATCH]
[--refind-mode {default,strict,off}]
[--min_trailing_support MIN_TRAILING_SUPPORT]
[--trailing_recursive TRAILING_RECURSIVE]
[--edge_support_threshold EDGE_SUPPORT_THRESHOLD]
Expand All @@ -65,9 +69,10 @@ usage: panaroo [-h] -i INPUT_FILES [INPUT_FILES ...] -o OUTPUT_DIR
[--high_var_flag CYCLE_THRESHOLD_MIN]
[--min_edge_support_sv MIN_EDGE_SUPPORT_SV]
[--all_seq_in_graph] [--no_clean_edges] [-a {core,pan}]
[--aligner {prank,clustal,mafft}] [--codons]
[--core_threshold CORE] [--core_entropy_filter HC_THRESHOLD]
[-t N_CPU] [--codon-table TABLE] [--quiet] [--version]
[--aligner {prank,clustal,mafft,none}] [--codons]
[--core_threshold CORE] [--core_subset SUBSET]
[--core_entropy_filter HC_THRESHOLD] [-t N_CPU]
[--codon-table TABLE] [--quiet] [--version]
panaroo: an updated pipeline for pangenome investigation
Expand Down Expand Up @@ -125,6 +130,9 @@ Matching:
(default=0.7)
--len_dif_percent LEN_DIF_PERCENT
length difference cutoff (default=0.98)
--family_len_dif_percent FAMILY_LEN_DIF_PERCENT
length difference cutoff at the gene family level
(default=0.0)
--merge_paralogs don't split paralogs
Refind:
Expand All @@ -134,6 +142,20 @@ Refind:
--refind_prop_match REFIND_PROP_MATCH
the proportion of an accessory gene that must be found
in order to consider it a match
--refind-mode {default,strict,off}
The stringency mode at which to re-find genes.
default:
Will re-find similar gene sequences. Allows for
premature stop codons and incorrect lengths to account
for misassemblies.
strict:
Prevents fragmented, misassembled, or potential
pseudogene sequences from being re-found.
off:
Turns off all re-finding steps.
Graph correction:
--min_trailing_support MIN_TRAILING_SUPPORT
Expand Down Expand Up @@ -170,13 +192,15 @@ Gene alignment:
-a {core,pan}, --alignment {core,pan}
Output alignments of core genes or all genes. Options
are 'core' and 'pan'. Default: 'None'
--aligner {prank,clustal,mafft}
--aligner {prank,clustal,mafft,none}
Specify an aligner. Options:'prank', 'clustal', and
default: 'mafft'
--codons Generate codon alignments by aligning sequences at the
protein level
--core_threshold CORE
Core-genome sample threshold (default=0.95)
--core_subset SUBSET Randomly subset the core genome to these many genes
(default=all)
--core_entropy_filter HC_THRESHOLD
Manually set the Block Mapping and Gathering with
Entropy (BMGE) filter. Can be between 0.0 and 1.0. By
Expand Down

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