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custom_parameters.txt
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custom_parameters.txt
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# qiime_parameters.txt
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_parameters.txt. Users should copy this file and edit copies of it.
###pick_otus_through_otu_table.py parameters###
# OTU picker parameters
pick_otus:otu_picking_method uclust
pick_otus:similarity 0.97
# Representative set picker parameters
pick_rep_set:rep_set_picking_method most_abundant
pick_rep_set:sort_by otu
# Multiple sequence alignment parameters
align_seqs:template_fp /home/qiime/core_set_aligned.fasta.imputed
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 /home/qiime/lanemask_in_1s_and_0s.txt
filter_alignment:allowed_gap_frac 0.999999
# Taxonomy assignment parameters
assign_taxonomy:assignment_method rdp
assign_taxonomy:confidence 0.8
# Phylogenetic tree building parameters
make_phylogeny:tree_method fasttree
###alpha_rarefaction.py parameters###
# Rarefaction parameters
multiple_rarefactions:num-reps 5
multiple_rarefactions:lineages_included False
# Alpha diversity parameters
alpha_diversity:metrics PD_whole_tree,observed_species,chao1
# Collate alpha
collate_alpha:example_path
# Make rarefaction plots parameters
make_rarefaction_plots:imagetype png
make_rarefaction_plots:resolution 75
###beta_diversity_through_3d_plots.py parameters###
# Beta diversity parameters
beta_diversity:metrics weighted_unifrac,unweighted_unifrac
# Make prefs file parameters
make_prefs_file:background_color black
make_prefs_file:mapping_headers_to_use Treatment,DOB
make_prefs_file:monte_carlo_dists 10
# Make 3D plot parameters
make_3d_plots:custom_axes
###jackknife_upgma.py parameters###
# Multiple Rarefactions
multiple_rarefactions_even_depth:num-reps 20
###parallel workflow###
# Parallel options
parallel:jobs_to_start 2
parallel:retain_temp_files False
parallel:seconds_to_sleep 1