# 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:similarity 0.97
#pick_otus:enable_rev_strand_match True

# Parallel options
#parallel:jobs_to_start	20
#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 /softwares/qiime_software/core_set_aligned.fasta.imputed
#align_seqs:alignment_method	pynast

# Alignment filtering (prior to tree-building) parameters
#filter_alignment:lane_mask_fp /softwares/qiime_software/lanemask_in_1s_and_0s
#filter_alignment:allowed_gap_frac	 0.999999

# Taxonomy assignment parameters
assign_taxonomy:id_to_taxonomy_fp /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
assign_taxonomy:reference_seqs_fp /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
assign_taxonomy:assignment_method	rdp
assign_taxonomy:blast_db
assign_taxonomy:confidence	0.8

# 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,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,shannon,simpson,fisher_alpha,goods_coverage,simpson_reciprocal,simpson_e

# 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