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# Set which tools to use in pipeline:
[pipeline]
# Options for Aligner:bwa / smalt / bowtie
aligner: bwa
# Options for variant_caller: samtoolswithpostalignbam / gatkhaplotypecaller /samtools
variant_caller: samtools
# Set bin folder path. Please make sure all the executables are placed in bin folder. Also make sure the path for individual tools are correct.
[bin_path]
binbase: /nfs/esnitkin/bin_group/variant_calling_bin/
[scheduler]
resources: nodes=1:ppn=4,pmem=4000mb,walltime=92:00:00
email: [email protected]
queue: fluxod
flux_account: esnitkin_fluxod
notification: a
# Set Parameters for individual tools. Set the binbase of each tool: This should be the folder name of respective tools where the executables for each resp. tool resides.
# Set parameter for Trimmomatic
[Trimmomatic]
trimmomatic_bin: /Trimmomatic/
adaptor_filepath: adapters/TruSeq3-Nextera_PE_combined.fa
seed_mismatches: 2
palindrome_clipthreshold: 30
simple_clipthreshold: 10
minadapterlength: 8
#change this to true and see the effect on alignment
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
[bwa]
bwa_bin: /bwa-0.7.12/
cores: 8
base_cmd: bwa
algorithm: mem
index: index
RG_header: -R
Mark_splithits: -M
[bowtie]
bowtie_bin: /bowtie2-2.2.6/
cores: 8
build_cmd: bowtie2-build
align_cmd: bowtie2
parameters: -k 1 --non-deterministic --end-to-end
[samtools]
samtools_bin: /samtools-1.2/
base_cmd: samtools
#minimum mapping quality
#change parameter S to -t SP and D to -t DP
mpileup_parameters: -ug -f
faiindex: faidx
#-q30 -B -E -C50
[bcftools]
bcftools_bin: /bcftools-1.2/
base_cmd: bcftools
call_parameters: -vg
[picard]
picard_bin: /picard-tools-2.5.0/
base_cmd: picard.jar
[gatk]
gatk_bin: /GenomeAnalysisTK-3.3-0/
base_cmd: GenomeAnalysisTK.jar
haplotype_parameters: -T HaplotypeCaller --genotyping_mode DISCOVERY
#changes: 12th August
gatk_filter1_parameter_expression: FQ < 40.00 && MQ > 20 && QUAL > 50 && DP > 15
gatk_filter2_parameter_expression: FQ < 0.025 && MQ > 50 && QUAL > 100 && DP > 15
#changed gatk_filter2_parameter_expression DP 15 from 10 that was used in VRE samples.
[vcftools]
#vcftools_perl_bin: /vcftools_0.1.12b/perl/
vcftools_bin: /vcftools_0.1.12b/bin/
tabix_bin: /tabix-0.2.6/
#vcftools_bin: /vcftools_0.1.12b/bin/
vcftools_perl_bin: /vcftools_0.1.12b/perl/
[qualimap]
qualimap_bin: /qualimap_v2.1/
base_cmd: qualimap
[bedtools]
bedtools_bin: /bedtools2-master/bin/
base_cmd: bedtools
version_for_coverage: /version_for_coverage/
[bioawk]
bioawk_bin: /bioawk-master/
base_cmd: bioawk
[fasttree]
fasttree_bin: /Fasttree_2.1.10/
#For Multithread fasttree; use FastTreeMP executable file
base_cmd: FastTree
[raxml]
raxml_bin: /raxml/
# Other raxml executable available to use: raxmlHPC-PTHREADS,raxmlHPC-PTHREADS-SSE3,raxmlHPC-SSE3
base_cmd: raxmlHPC-SSE3
parameters: -f a -x 12345 -p 12345 -N autoMRE -m GTRCAT -T 20
[gubbins]
# Change this path to wherever gubbins is located/installed. Right now, installed using conda from anaconda3 package installed in bin_group.
gubbins_bin: /nfs/esnitkin/bin_group/anaconda3/bin/
base_cmd: run_gubbins.py
[SNP_filters]
filter_criteria: snitkin_filters
# Other Criterias: SPANDx_filters, loose_filters, snitkin_filters
[snitkin_filters]
avg_depth: no
# If AVG_DEPTH is yes, the below DP threshold will be ignored. Instead, LOW_DEPTH and HIGH_DEPTH filter parameter will be used.
# Filter variants with Depth less than the below threshold
dp: 9
# A value of 2 means that regions with less than half of the average coverage of the entire genome will fail
low_depth: 2
# A value of 5 means that regions with 5x depth greater than the average coverage will fail
high_depth: 5
# Filter variants with FQ(Consensus Quality) greater than the below threshold
fq: 0.025
fq2: 0.025
# Filter variants with MQ(Root Mean Square Quality) less than the below threshold
mq: 50
# Filter variants with Variant QUAL less than the below threshold
qual: 100
# Filter Variants that are proximate to each other
prox: 10
#CLUSTER_SNP: 3
#CLUSTER_WINDOW_SNP: 10
#MLEAF_SNP: 0.95
#QD_SNP: 10.0
#FS_SNP: 10.0
#HAPLO_SNP: 20.0
##SNP annotations
[snpeff]
snpeff_bin: /snpEff/
base_cmd: snpEff.jar
snpeff_parameters: -d -no-downstream -no-upstream
dataDir: /data/
########################################################################################################################
# Reference Genome to be used for pipeline
# Set path for already indexed reference genome
# Most Frequently used reference genomes
# Name of the reference genome. Provide this value with -index_name argument.
[KPNIH1]
# Name of reference genome fasta file.
Ref_Name: KPNIH1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPNIH1/
# Name of the reference genome. Provide this value with -index_name argument.
[aus]
# Name of reference genome fasta file.
Ref_Name: Efae_aus0004_genome.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/aus/
[MRSA_USA_300]
# Name of reference genome fasta file.
Ref_Name: MRSA_USA_300.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/MRSA_USA_300/
[FPR3757]
# Name of reference genome fasta file.
Ref_Name: FPR3757.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/FPR3757/
[MRSA_USA_100]
# Name of reference genome fasta file.
Ref_Name: MRSA_USA_100_1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/MRSA_USA_100/
[CDIFF_630]
# Name of reference genome fasta file.
Ref_Name: cdiff_630.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/CDIFF_630/
[CFT073]
# Name of reference genome fasta file.
Ref_Name: EscherichiacoliCFT073.fna
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/CFT073
[paris]
# Name of reference genome fasta file.
Ref_Name: Paris.fna
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/legionella/paris/
#########################################################################
#Name of the reference genome. Provide this value with -index_name option.
[KPC_264]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_264_contigs_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_264/
## Efaecalis and Efaecium Reference Genomes
# Name of the reference genome. Provide this value with -index_name argument.
[EPI51]
# Name of reference genome fasta file.
Ref_Name: Efae_EPI51_060509_genome.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/EPI51/
# Name of the reference genome. Provide this value with -index_name argument.
[EnGen0178]
# Name of reference genome fasta file.
Ref_Name: EnGen0178_genome.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/EnGen0178/
# Name of the reference genome. Provide this value with -index_name argument.
[EnGen0377]
# Name of reference genome fasta file.
Ref_Name: EnGen0377_genome.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/EnGen0377/
[ECNIH3]
# Name of reference genome fasta file.
Ref_Name: ECNIH3.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference//ECNIH3/
[ECNIH2]
# Name of reference genome fasta file.
Ref_Name: ECNIH2.fa
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference//ECNIH2/
[Efaecalis_V583]
# Name of reference genome fasta file.
Ref_Name: Efaecalis_V583.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference//Efaecalis_V583//
[Efaecium_Aus0085]
# Name of reference genome fasta file.
Ref_Name: Efaecium_Aus0085.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference//Efaecium_Aus0085/
## MRSA Reference Genomes
[MRSA_8058]
# Name of reference genome fasta file.
Ref_Name: MRSA_8058.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/MRSA_8058
[6338]
# Name of reference genome fasta file.
Ref_Name: 6338_R1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/6338
[8061]
# Name of reference genome fasta file.
Ref_Name: 8061_R1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/8061
[KP_mrsa_41]
# Name of reference genome fasta file.
Ref_Name: KP_mrsa_41_1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KP_mrsa_41
[KP_mrsa_67]
# Name of reference genome fasta file.
Ref_Name: KP_mrsa_67_1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KP_mrsa_67
[KP_mrsa_41_2]
# Name of reference genome fasta file.
Ref_Name: KP_mrsa_41.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_MRSA_analysis/ISmapper/2016_04_19_analysis_2/KP_mrsa_41_analysis/
## Cdiff Reference Genomes
[H102]
# Name of reference genome fasta file.
Ref_Name: PCMP_H102_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H102/
[H128]
# Name of reference genome fasta file.
Ref_Name: PCMP_H128_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H128/
[H159]
# Name of reference genome fasta file.
Ref_Name: PCMP_H159_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H159/
[H298]
# Name of reference genome fasta file.
Ref_Name: PCMP_H298_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H298/
[H304]
# Name of reference genome fasta file.
Ref_Name: PCMP_H304_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H304/
[H358]
# Name of reference genome fasta file.
Ref_Name: PCMP_H358_R1_l500_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/H358/
########################################################################################################################
# KPC Cluster Specific Reference Genomes
[313]
# Name of reference genome fasta file.
Ref_Name: 313_R1_001_final_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_108]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_108_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_110]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_110_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_157]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_157_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_212]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_212_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_216]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_216_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_233]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_233_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_412]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_412_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_48]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_48_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_52]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_52_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_586]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_586_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
[Rush_KPC_653]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_653_R1_l500_contigs.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_KPC_LTACH_analysis/Analysis/Project_KPC_all_KPC_2008+Hiseq+Latest/2017-01-17-Variant-Calling_Strain_Specific/data/reference/
##Ecoli Reference Genomes
[Ecoli_CD306]
# Name of reference genome fasta file.
Ref_Name: Ecoli_CD306.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Ecoli_CD306
[Escherichia_coli_K_12]
# Name of reference genome fasta file.
Ref_Name: Escherichia_coli_K_12.fna
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Nursing_home/e_coli/Escherichia_coli_K_12/
##Ecoli NH cluster-based Reference Genomes
[3425-5015-0-R2X]
# Name of reference genome fasta file.
Ref_Name: 3425-5015-0-R2X_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3425-5015-0-R2X
[3940-B014-14-RX-TIP14]
# Name of reference genome fasta file.
Ref_Name: 3940-B014-14-RX-TIP14__ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3940-B014-14-RX-TIP14
[1677-J011-1-OX-TIP14]
# Name of reference genome fasta file.
Ref_Name: 1677-J011-1-OX-TIP14_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/1677-J011-1-OX-TIP14
##Saureus NH cluster-based Reference Genomes
[3850-B013-90-R-TIPmmrsa]
# Name of reference genome fasta file.
Ref_Name: 3850-B013-90-R-TIPmmrsa_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3850-B013-90-R-TIPmmrsa
[3933-A018-14-W-TIPmmrsa]
# Name of reference genome fasta file.
Ref_Name: 3933-A018-14-W-TIPmmrsa_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3933-A018-14-W-TIPmmrsa
[803-A001-120-N-MRSA-TIP]
# Name of reference genome fasta file.
Ref_Name: 803-A001-120-N-MRSA-TIP__ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/803-A001-120-N-MRSA-TIP
##Efaecium NH cluster-based Reference Genomes
[3399-4058-0-RVRE]
# Name of reference genome fasta file.
Ref_Name: 3399-4058-0-RVRE_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3399-4058-0-RVRE
##Efaecium NH cluster-based Reference Genomes
[3399-4058-0-RVRE_latest]
# Name of reference genome fasta file.
Ref_Name: 3399-4058-0-RVRE_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Nursing_home/efaecium/cluster_1_3399-4058-0-RVRE/
##Efaecalis NH cluster-based Reference Genomes
[1726-E049-14-O-TIPmvre]
# Name of reference genome fasta file.
Ref_Name: 1726-E049-14-O-TIPmvre_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/1726-E049-14-O-TIPmvre
[3401-5015-0-H1VRE]
# Name of reference genome fasta file.
Ref_Name: 3401-5015-0-H1VRE_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3401-5015-0-H1VRE
[3954-F065-30-G-TIPmvre]
# Name of reference genome fasta file.
Ref_Name: 3954-F065-30-G-TIPmvre__ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/3954-F065-30-G-TIPmvre
[7605-4117-0-HVRE]
# Name of reference genome fasta file.
Ref_Name: 7605-4117-0-HVRE_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/7605-4117-0-HVRE
##Mmorgannii reference genome
[Morganella_morganii_strain_FDAARGOS_63]
# Name of reference genome fasta file.
Ref_Name: Morganella_morganii_strain_FDAARGOS_63.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Nursing_home/mmorganii/Morganella_morganii_strain_FDAARGOS_63/
##P mirabilis reference genome
[Proteus_mirabilis_strain_FDAARGOS_60]
# Name of reference genome fasta file.
Ref_Name: Proteus_mirabilis_strain_FDAARGOS_60.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Nursing_home/pmirabilis/Proteus_mirabilis_strain_FDAARGOS_60/
## P aeru reference genome
[Pseudomonas_aeruginosa_FRD1]
# Name of reference genome fasta file.
Ref_Name: Pseudomonas_aeruginosa_FRD1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Nursing_home/paeru/Pseudomonas_aeruginosa_FRD1/
#RNA Seq Reference Genomes
[HM14]
# Name of reference genome fasta file.
Ref_Name: HM14.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM17]
# Name of reference genome fasta file.
Ref_Name: HM17.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM1]
# Name of reference genome fasta file.
Ref_Name: HM1.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM26]
# Name of reference genome fasta file.
Ref_Name: HM26.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM27]
# Name of reference genome fasta file.
Ref_Name: HM27.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM3]
# Name of reference genome fasta file.
Ref_Name: HM3.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM43]
# Name of reference genome fasta file.
Ref_Name: HM43.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM46]
# Name of reference genome fasta file.
Ref_Name: HM46.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM54]
# Name of reference genome fasta file.
Ref_Name: HM54.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM56]
# Name of reference genome fasta file.
Ref_Name: HM56.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM57]
# Name of reference genome fasta file.
Ref_Name: HM57.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM60]
# Name of reference genome fasta file.
Ref_Name: HM60.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM65]
# Name of reference genome fasta file.
Ref_Name: HM65.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM66]
# Name of reference genome fasta file.
Ref_Name: HM66.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM67]
# Name of reference genome fasta file.
Ref_Name: HM67.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM68]
# Name of reference genome fasta file.
Ref_Name: HM68.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM6]
# Name of reference genome fasta file.
Ref_Name: HM6.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM7]
# Name of reference genome fasta file.
Ref_Name: HM7.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
[HM86]
# Name of reference genome fasta file.
Ref_Name: HM86.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/Ali/Project_RNA_seq/Reference_genomes/
## Legionella Reference Genomes
## KPC Ltach cluster
[cluster_1_Rush_KPC_350_S8_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_350_S8__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_1_Rush_KPC_350_S8_
[cluster_2_Rush_KPC_21_S35_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_21_S35__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_2_Rush_KPC_21_S35_/
[cluster_3_Rush_KPC_159_S30_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_159_S30__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_3_Rush_KPC_159_S30_/
[cluster_4_Rush_KPC_226_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_226_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_4_Rush_KPC_226_R1/
[cluster_5_Rush_KPC_191_S49_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_191_S49__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_5_Rush_KPC_191_S49_/
[cluster_6_Rush_KPC_418_S23_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_418_S23__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_6_Rush_KPC_418_S23_/
[cluster_7_Rush_KPC_87_S3_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_87_S3__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_7_Rush_KPC_87_S3_/
[cluster_8_Rush_KPC_110_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_110_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_8_Rush_KPC_110_R1/
[cluster_9_Rush_KPC_162_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_162_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_9_Rush_KPC_162_R1/
[cluster_10_Rush_KPC_340_S13_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_340_S13__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_10_Rush_KPC_340_S13_/
[cluster_11_Rush_KPC_573_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_573_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_11_Rush_KPC_573_R1/
[cluster_12_Rush_KPC_615_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_615_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_12_Rush_KPC_615_R1/
[cluster_13_Rush_KPC_348_S25_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_348_S25__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_13_Rush_KPC_348_S25_/
[cluster_14_Rush_KPC_216_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_216_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_14_Rush_KPC_216_R1/
[cluster_15_Rush_KPC_108_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_108_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_15_Rush_KPC_108_R1/
[cluster_16_Rush_KPC_52_R1]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_52_R1_final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_16_Rush_KPC_52_R1/
[cluster_17_Rush_KPC_60_S27_]
# Name of reference genome fasta file.
Ref_Name: Rush_KPC_60_S27__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/KPC_LTACH_clusters/cluster_17_Rush_KPC_60_S27_/
## Ecoli KO analysis
[NC101-WT]
# Name of reference genome fasta file.
Ref_Name: NC101-WT__final_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/NC101-WT/
[Ecoli_KO_Gaps]
# Name of reference genome fasta file.
Ref_Name: Gaps_annotations_ordered.fasta
# path to the reference genome fasta file.
Ref_Path: /scratch/esnitkin_fluxod/apirani/Project_Ecoli_KO/Analysis/2017_11_07_Ecoli_KO_Gap_variant_calling/
[Ecoli_KO_colibactin]
# Name of reference genome fasta file.
Ref_Name: E_coli_colibactin_gene.fasta
# path to the reference genome fasta file.
Ref_Path: /scratch/esnitkin_fluxod/apirani/Project_Ecoli_KO/Analysis/2017_11_07_Ecoli_KO_colibactin_gene_variant_calling/
##LTACH latest clusters
/home/apirani/bin/reference/KPC_LTACH_clusters_2/cluster_1_Rush_KPC_194/Rush_KPC_194_contigs_ordered.fasta
/home/apirani/bin/reference/KPC_LTACH_clusters_2/cluster_2_Rush_KPC_350/Rush_KPC_350_S8_contigs_ordered.fasta
/home/apirani/bin/reference/KPC_LTACH_clusters_2/cluster_8_Rush_KPC_21/Rush_KPC_21_S35_contigs_ordered.fasta