/
config.sh
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/
config.sh
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#!/bin/bash
# scripts for 16S data analysis
#
# originally by Ruben Garrido-Oter
# garridoo@mpipz.mpg.de
# working_dir is the folder where (intermediate) results are stored
working_dir="/biodata/dep_psl/grp_psl/garridoo/cc/results"
# data_dir is the folder where the raw data (and maping file) are deposited
data_dir="/biodata/dep_psl/grp_psl/garridoo/cc/data"
# paths to relevant reference database files
refdata_dir="/projects/dep_psl/grp_psl/garridoo/16S/ref_data"
gg_core_db=$refdata_dir"/gg_13_8_otus/rep_set/97_otus.fasta"
gg_core_aligned_db=$refdata_dir"/gg_13_8_otus/rep_set_aligned/97_otus.fasta"
gg_taxonomy=$refdata_dir"/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt"
gold_db=$refdata_dir"/cs_gold.fa"
# path to folder containing usearch binary and python scripts
usearch_dir="/projects/dep_psl/grp_psl/garridoo/16S/usearch"
### debug
output=$working_dir"/output.txt"
logfile=$working_dir"/log.txt"
### parameters
# number of threads for parallel steps
n_cores=30
# min Phred score for quality control
phred=25
# max. barcode errors
bc_err=0
# min. number of reads for a given OTU
min_size=2
# identity threshold for OTU clustering
id_threshold=0.97
# min length of alingment required to sequences in the database
min_id_aln=0.75
# subsampling depth used for alpha-diversity
subsampling_depth=500
# OTU clustering method
tax_method="uclust"