# -------------------- lOTUs configuration file
# Progams Pathways  -- have to be set before first use
# /YY/ is an abbreviation for the complete system path to specific program, if the program is in the system path, no absolute path needs to be set
# only usearch and rdp are required - usearch binaries (e.g. "usearch	/home/user/bin/usearch/./usearch7.0.959_i86linux64")

#sdm - essential C++ part of the LotuS pipeline
sdm bin/sdm
#LCA implementation in C++, not essential
LCA bin/LCA
#rarefaction toolkit
rtk bin/rtk
#R helper scripts
dada2R bin/R/dada2_pip.R
phyloLnk bin/R/l2phyloseq.R
LULUR bin/R/LULU.R
ASVcl bin/R/ASV_clustering.R

#usearch clustering & chimera checking program
usearch usearch_11
#swarm clustering program
swarm swarm
#cd-hit-est clustering program
cd-hit cd-hit-est
#vsearch chimera checking, OTU clustering and mapping
vsearch vsearch
#dnaclust ref based OTU clustering
dnaclust dnaclust
minimap2 minimap2


#RDP multiclassifier java archieve (e.g. /YY/MultiClassifier.jar)
#alternatively leave this "" and set environmental variable to RDP_JAR_PATH, as described in RDP documentary
multiRDPjar MultiClassifier.jar
RDPjar rdp_classifier


#Blastn+ binary (e.g. /YY/ncbi-blast-2.2.XX+/bin/blastn)
blastn blastn
makeBlastDB makeblastdb
#lambda binaries used for ref taxa searches
lambda_index lambda_indexer
lambda lambda
lambda3 lambda3

#clustalo multiple alignment binary (e.g. /YY/clustaloBin-1.2.0-OS-x86_64)
clustalo clustalo-1.2.0-Ubuntu-x86_64
mafft mafft.bat

#FastTree binary - for speed improvements /YY/FastTReeMP recommended -- requires clustalo
fasttree FastTreeMP
#iqTree binary - more precise than fasttree at almost equal speeds
iqtree iqtree2

#flash - required for merging big fastq files
flashBin flash

#ITSX - required to only retain OTU's matching an ITS
itsx ITSx
#hmmsearch
hmmsearch hmmscan

#V-xtractor
vxtractorHMMs bin/vxtr/HMMs/
vxtractor bin/vxtr/vxtractor.pl

# --------------------
#   databases
#reference database for ref chimera filtering - suggested is gold.fa for bacteria SSU and UNITE resources for fungal ITS
UCHIME_REFDB DB//rdp_gold.fa
UCHIME_REFDB_LSU DB//SLV_119_LSU.fa
UCHIME_REFDB_ITS DB//ITS_chimera/uchime_sh_refs_dynamic_original_985_11.03.2015.fasta
UCHIME_REFDB_ITS2 DB//ITS_chimera/ITS1_ITS2_datasets/uchime_sh_refs_dynamic_develop_985_11.03.2015.ITS2.fasta
UCHIME_REFDB_ITS1 DB//ITS_chimera/ITS1_ITS2_datasets/uchime_sh_refs_dynamic_develop_985_11.03.2015.ITS1.fasta

#outdated - greengenes fasta ref database - requires blastn
TAX_REFDB_GG DB//gg_13_5.fasta
#outdated - greengenes taxnomic assignments for ref fasta database - requires blastn
TAX_RANK_GG DB//gg_13_5_taxonomy

#greengenes2 fasta ref database - requires blastn
TAX_REFDB_GG2 DB//GG2.2022.10.fasta
#greengenes2 taxnomic assignments for ref fasta database - requires blastn
TAX_RANK_GG2 DB//GG2.2022.10.tax

#SILVA SSU fasta ref database - requires blastn
TAX_REFDB_SSU_SLV DB//SLV_138_SSU.fasta
#SILVA SSU taxnoomic assignments for ref fasta database - requires blastn
TAX_RANK_SSU_SLV DB//SLV_138_SSU.tax
#SILVA LSU fasta ref database - requires blastn
TAX_REFDB_LSU_SLV DB//SLV_138_LSU.fasta
#SILVA LSU taxonomic assignments for ref fasta database - requires blastn
TAX_RANK_LSU_SLV DB//SLV_138_LSU.tax
#UNITE ITS fasta ref database - requires blastn
TAX_REFDB_ITS_UNITE DB//UNITE/sh_refs_qiime_ver8_99_s_all_02.02.2019.fasta
#UNITE ITS fasta ref tax - requires blastn
TAX_RANK_ITS_UNITE DB//UNITE/sh_taxonomy_qiime_ver8_99_s_all_02.02.2019.txt
#reference database with phiX, to check for illumina platform phiX remainders
REFDB_PHIX DB//phiX.fasta
#HITdb SSU database
TAX_REFDB_HITdb DB//HITdb/HITdb_sequences.fna
TAX_RANK_HITdb DB//HITdb/HITdb_taxonomy.txt
#PR2 LSU database
TAX_REFDB_PR2 DB//PR2/gb203_pr2_all_10_28_99p.fasta
TAX_RANK_PR2 DB//PR2/PR2_taxonomy.txt
#ref DB for utax ITS + 16S
TAX_REFDB_SSU_UTAX DB//utaxref/rdp_16s_trainset15/
TAX_REFDB_ITS_UTAX DB//utaxref/unite_v7/
TAX_REFDB_BEE DB//beeTax/beeTax.fna
TAX_RANK_BEE DB//beeTax/beeTax.txt
infernal bin//infernal-1.1.2-linux-intel-gcc/binaries/

#KSGP database.. combination of several DBs, supplemented by environmental full length 16S/18S sequences
TAX_RANK_KSGP DB//KSGP_v1.0.fasta
TAX_REFDB_KSGP DB//KSGP_v1.0.tax


# --------------------
#  LotuS parameters
#unique identifier, can be used for debugging support
UID ??
#Threshold used in blast LCA algorithm to delimit taxonomic assignments, if OTU sequence is below %id to reference sequence. This can be delimited to 5 taxanomic levels (separated by ","): species, genus, family, class, order, phylum. E.g.: 97,95,92,90,88,85
#IdentityThresholds 97,95,93,91,88,78
#updated based on Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews. Microbiology 12, 635–645 (2014).: Table 1, Min seq id, uprounded
IdentityThresholds 97,95,88,83,81,78

#This will check for more & less important updates each time lotus is run. Note that we will never track your LotuS usuage in any way, this is purely a convenience option if desired.
CheckForUpdates 0
