config~

[bin_path]
binbase = /nfs/esnitkin/bin_group/assembly_bin/

[Trimmomatic]
trimmomatic_bin = /Trimmomatic/
#adaptor_filepath = adapters/NexteraPE-PE.fa
adaptor_filepath = adapters/TruSeq3-Nextera_PE_combined.fa
#adaptor_filepath = adapters/TruSeq3-PE.fa
adaptor_filepath_se = adapters/TruSeq3-SE.fa
seed_mismatches = 2
palindrome_clipthreshold = 30
simple_clipthreshold = 10
minadapterlength = 8
keep_both_reads = true
window_size = 4
window_size_quality = 20
minlength = 40
headcrop_length = 0
colon = :
targetlength = 125
crop_length = 40
f_p = /forward_paired.fq.gz
f_up = /forward_unpaired.fq.gz
r_p = /reverse_paired.fq.gz
r_up = /reverse_unpaired.fq.gz

[check_clean]
paired = 1
unpaired = 1

[spades]
spades_bin = /SPAdes-3.10.1-Linux/bin/
base_cmd = spades.py
threads = 
spades_parameters = --careful
plasmid_spades_parameters = --plasmid
contigs_path = /spades_results/contigs.fasta
scaffolds_path = /spades_results/scaffolds.fasta
plasmid_contigs_path = /spades_plasmid_results/contigs.fasta
plasmid_scaffolds_path = /spades_plasmid_results/scaffolds.fasta

[quast]
quast_bin = /quast/
base_cmd = quast.py
quast_parameters = --threads 8

[reapr]
reapr_bin = /Reapr_1.0.17/
base_cmd = reapr
reapr_parameters = 
perfectfrombam_parameters = perfect 100 500 3 4 76

[abacas]
abacas_bin = /PAGIT/ABACAS/
base_cmd = abacas.1.3.1.pl
abacas_parameters = -p nucmer -b -d -a -m

[mummer]
mummer_bin = /MUMmer3.23/

[prokka]
prokka_bin = /prokka-1.11/bin/
base_cmd = prokka
prokka_parameters = -kingdom Bacteria --force --rfam

[ariba]
ariba_bin = /nfs/esnitkin/bin_group/anaconda3/bin/
base_cmd = ariba
ariba_amr_db = /nfs/esnitkin/bin_group/ariba/database/custom_new/out.card.proteus.prepareref/
ariba_mlst_db = /nfs/esnitkin/bin_group/ariba/database/MLST_db/e_coli_MLST_alleles_db/e_coli_mlst/ref_db/
#ariba_mlst_db = /nfs/esnitkin/bin_group/ariba/database/MLST_db/KP_MLST/ref_db/

[bioawk]
bioawk_bin = /bioawk/
base_cmd = bioawk

[cd-hit]
cd_hit_bin = /nfs/esnitkin/bin_group/cd-hit/
base_cmd = cd-hit

[velvet]
velvet_bin = 
base_cmd = 
velvet_parameters = 
contigs_path = /velvet_results/contigs.fa
scaffolds_path = 

[XXXX]
ref_name = XXXX
ref_path = XXXX

[KPNIH1]
ref_name = KPNIH1.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPNIH1/

[MRSA_USA_300]
ref_name = MRSA_USA_300.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/MRSA_USA_300

[CDIFF_630]
ref_name = cdiff_630.fasta
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/CDIFF_630/

[CFT073]
ref_name = EcoliCFT073.fna
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/CFT073/

[paris]
ref_name = Paris.fna
ref_path = /nfs/esnitkin/bin_group/variant_calling_bin/reference/paris/