# qiime_parameters.txt
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_parameters.txt. Users should copy this file and edit copies of it.

# split libraries parameters
split_libraries:min-seq-length
split_libraries:max-seq-length
split_libraries:trim-seq-length
split_libraries:min-qual-score
split_libraries:keep-primer
split_libraries:keep-barcode
split_libraries:max-ambig
split_libraries:max-homopolymer
split_libraries:max-primer-mismatch
split_libraries:barcode-type
split_libraries:max-barcode-errors
split_libraries:start-numbering-at
split_libraries:remove_unassigned	True
split_libraries:disable_bc_correction
split_libraries:qual_score_window
split_libraries:discard_bad_windows
split_libraries:disable_primers
split_libraries:reverse_primers
split_libraries:record_qual_scores

# OTU picker parameters
pick_otus:otu_picking_method	uclust
pick_otus:clustering_algorithm	furthest
pick_otus:max_cdhit_memory	400
pick_otus:refseqs_fp
pick_otus:blast_db
pick_otus:similarity	0.97
pick_otus:max_e_value	1e-10
pick_otus:prefix_prefilter_length
pick_otus:trie_prefilter
pick_otus:prefix_length
pick_otus:suffix_length
pick_otus:optimal_uclust
pick_otus:exact_uclust
pick_otus:user_sort
pick_otus:suppress_presort_by_abundance_uclust
pick_otus:suppress_new_clusters
pick_otus:suppress_uclust_stable_sort
pick_otus:max_accepts
pick_otus:max_rejects
pick_otus:word_length
pick_otus:stepwords
pick_otus:suppress_uclust_prefilter_exact_match

# Parallel options
parallel:jobs_to_start	1
parallel:retain_temp_files	False
parallel:seconds_to_sleep	60

# Representative set picker parameters
pick_rep_set:rep_set_picking_method	first
pick_rep_set:sort_by	otu

# Multiple sequence alignment parameters
align_seqs:template_fp
align_seqs:alignment_method	pynast
align_seqs:pairwise_alignment_method	uclust
align_seqs:blast_db
align_seqs:min_length	150
align_seqs:min_percent_id	75.0

# Alignment filtering (prior to tree-building) parameters
filter_alignment:lane_mask_fp
filter_alignment:allowed_gap_frac	 0.999999
filter_alignment:remove_outliers	False
filter_alignment:threshold	3.0

# Taxonomy assignment parameters
assign_taxonomy:id_to_taxonomy_fp
assign_taxonomy:reference_seqs_fp
assign_taxonomy:assignment_method	rdp
assign_taxonomy:blast_db
assign_taxonomy:confidence	0.8
assign_taxonomy:e_value	0.001

# Phylogenetic tree building parameters
make_phylogeny:tree_method	fasttree
make_phylogeny:root_method	tree_method_default

# Beta diversity parameters
beta_diversity:metrics	weighted_unifrac,unweighted_unifrac,dist_bray_curtis

# Make 3D plot parameters
make_3d_plots:custom_axes
make_3d_plots:ellipsoid_smoothness   1

# Rarefaction parameters
multiple_rarefactions:num-reps	10
multiple_rarefactions:depth
multiple_rarefactions:lineages_included	False

# Even-depth rarefaction parameters
multiple_rarefactions_even_depth:num-reps	100

# Alpha diversity parameters
alpha_diversity:metrics	PD_whole_tree,chao1,observed_species

# Make rarefaction plots parameters
make_rarefaction_plots:imagetype	png
make_rarefaction_plots:resolution	75
make_rarefaction_plots:background_color	white
make_rarefaction_plots:prefs_path

# Collate alpha
collate_alpha:example_path

# OTU category significance
otu_category_significance:test
otu_category_significance:filter	3
otu_category_significance:threshold
otu_category_significance:otu_include_fp