config_template.txt

[project]
##number of cpu
cpu=4
##store output to [outpath]/[projname] 
outpath=
projname=testPoreEDGE
projdesc=lambda genome
projid=
projcode=
projowner=
projrunhost=

[Download Fastq]
DoFastqDownload=auto

[Download SRA]
DoSRADownload=0
## SRA accessions ByrRun, ByExp, BySample, ByStudy 
SRA_id=SRX674271

[Count Fastq]
DoCountFastq=auto
fastq_source=not

[Quality Trim and Filter]
## boolean, 1=yes, 0=no
DoQC=1
## phred encoding offset,  0 for autocheck
qc_phred_offset=0
##Targets quality level for trimming
q=5
##Trimmed sequence length will have at least minimum length 
min_L=50
##Average quality cutoff
avg_q=0
##"N" base cutoff.  Trimmed read has more than this number of continuous base "N" will be discarded. 
n=1
##Low complexity filter ratio, Maximum fraction of mono-/di-nucleotide sequence
lc=0.85
## Trim reads with adapters or contamination sequences
adapter=/PATH/adapter.fasta
porechop=0
## Trim polyA (>15)
polyA=0
## Cut # bp from 5 end before quality trimming/filtering 
5end=0
## Cut # bp from 3 end before quality trimming/filtering 
3end=0

[Join PE Reads]
DoJoinPE=0
fastqjoin-maxdiff=8
fastqjoin-minoverlap=6
fastqjoin-usejoined-only=0

[Host Removal]
## boolean, 1=yes, 0=no
DoHostRemoval=1
## Use more Host=  to remove multiple host reads
Host=/PATH/all_chromosome.fasta
similarity=90

[Assembly]
## boolean, 1=yes, 0=no
DoAssembly=1
#Bypass assembly and use pre-assembled contigs
assembledContigs=
inputContigs=
minContigSize=200
## spades, idba_ud, megahit, unicycler, or lrasm 
assembler=idba_ud
idbaOptions="--pre_correction  --mink 31"
## for spades
## support algorithm: default, singlecell,metagenome,plasmid,rna
SpadesAlgorithm=default
SpadesPacbioFile=
SpadesNanoporeFile=
## for megahit
megahit_preset=meta
## for unicycler
unicycler_mode=normal
unicycler_lreads_file=
unicycler_min_lreads=2000
## for lrasm
lrasm_num_consensus=3
lrasm_preset=ont
lrasm_ec=1
# support miniasm and wtdbg2
lrasm_algorithm=miniasm

[Reads Mapping To Contigs]
# Reads mapping to contigs
DoReadsMappingContigs=auto
## support bowtie or bwa
edge-r2c-aligner=bowtie
edge-r2c-aligner-options=
r2c_extract_unmapped=0

[Reads Mapping To Reference]
# Reads mapping to reference
DoReadsMappingReference=0
## support bowtie or bwa
edge-r2g-aligner=bowtie
edge-r2g-aligner-options=
r2g_max_clip=50
# reference genbank or fasta file
reference=
MapUnmappedReads=0
r2g_extract_mapped=0
r2g_extract_unmapped=0
r2g_get_consensus=0
r2g_consensus_min_mapQ=10
r2g_consensus_max_cov=300
r2g_consensus_alt_prop=0.5
r2g_consensus_min_cov=5
r2g_consensus_min_baseQ=20
r2g_variant_call=1
r2g_variant_call_ploidy=haploid

[Reads Taxonomy Classification]
## boolean, 1=yes, 0=no
DoReadsTaxonomy=1
## If reference genome exists, only use unmapped reads to do Taxonomy Classification. Turn on AllReads=1 will use all reads instead.
AllReads=0
enabledTools=gottcha-genDB-b,gottcha-speDB-b,gottcha-strDB-b,gottcha-genDB-v,gottcha-speDB-v,gottcha-strDB-v,gottcha2-speDB-b,metaphlan2,bwa,kraken2,diamond
splitrim-minq=20
custom-gottcha-genDB-b=
custom-gottcha-speDB-b=
custom-gottcha-strDB-b=
custom-gottcha-genDB-v=
custom-gottcha-speDB-v=
custom-gottcha-strDB-v=
custom-gottcha2-speDB-b=
custom-gottcha2-genDB-v=
custom-gottcha2-speDB-v=
custom-bwa-db=
custom-metaphlan-db=
custom-kraken-db=
custom-pangia-db=
custom-diamond-db=

[Contigs Mapping To Reference]
# Contig mapping to reference
DoContigMapping=auto
## identity cutoff
identity=85
MapUnmappedContigs=0

[Variant Analysis]
DoVariantAnalysis=auto

[Contigs Taxonomy Classification]
DoContigsTaxonomy=1

[Contigs Annotation]
## boolean, 1=yes, 0=no
DoAnnotation=1
# kingdom: Archaea Bacteria Mitochondria Viruses
kingdom=Bacteria
contig_size_cut_for_annotation=700
## support tools: Prokka or RATT
annotateProgram=Prokka
annotateSourceGBK=
DoKeggOmicsView=

[Contigs Binning]
DoBinning=0
contig_size_cut_for_binning=1000
binning-max-itr=50
binning-prob=0.9
binning-markerset=107
binning-abund-file=

[ProPhage Detection]
DoProPhageDetection=1

[Secondary Metabolite Analysis]
DoSMA=0
antismash-taxon=bacteria
antismash-clusterblast=
antismash-subclusterblast=
antismash-knownclusterblast=
antismash-smcogs=
antismash-asf=
antismash-fullhmm=
antismash-cassis=
antismash-tta=
antismash-borderpredict=
antismash-inclusive=
antismash-inclusive-cdsnr=5
antismash-inclusive-threshold=0.6
antismash-inclusive-npfams=5

[Phylogenetic Analysis]
DoSNPtree=1
## Availabe choices are Ecoli, Yersinia, Francisella, Brucella, Bacillus
SNPdbName=Ecoli
## List of genome name from NCBI genomes see $EDGE/edge_ui/data/Ref_list.json
SNPGenomes=
SNPGenomesFiles=
## A refrence genoem from above two options for reads/contigs mapping
SNPrefGenome=
## FastTree or RAxML
treeMaker=FastTree
## SRA accessions ByrRun, ByExp, BySample, ByStudy
SNP_SRA_ids=
PhaMEbootstrap=0
PhaMEbootstrap_num=100

[Gene Family Analysis]
DoReadsSpecialtyGenes=0
DoORFsSpecialtyGenes==0
SpecialtyGenesSearchTool=rapsearch2
ShortBREDMinPercIdentity=
ShortBREDMinPercLength=

[Primer Validation]
DoPrimerValidation=1
maxMismatch=1
# primer fasta file
primer=

[Primer Adjudication]
## boolean, 1=yes, 0=no
DoPrimerDesign=0
## desired primer tm
tm_opt=59
tm_min=57
tm_max=63
## desired primer length
len_opt=18
len_min=20
len_max=27
## reject primer having Tm < tm_diff difference with background Tm
tm_diff=5
## display # top results for each target
top=5

[Qiime analysis]
DoQiimeAnalysis=0
## Greengenes, SILVA, SILVA-V3-V4 or ITS
qiime_amplicon_type=SILVA
qiime_input_dir=
qiime_mapping_file=
qiime_barcode_file=
qiime_phred_offset=33
qiime_sampling_depth=1000
qiime_qcMethod=dada2
qiime_trimLeftForward=20
qiime_trimLeftReverse=20
qiime_truncLenForward=250
qiime_truncLenReverse=250
qiime_trimLen=20
qiime_truncLen=0
qiime_autoDepth=1
qiime_q_threshold=4
qiime_max_n=1
qiime_min_per_read_length_fraction=0.5

[DETEQT analysis]
DoDETEQT=0
targetedNGS_ref=
targetedNGS_input_dir=
targetedNGS_sample_file=
targetedNGS_q_cutoff=0.8145
targetedNGS_depth_cutoff=1000
targetedNGS_len_cutoff=100
targetedNGS_mode=PE
targetedNGS_platform=illumina
targetedNGS_expectedCoverage=1
targetedNGS_expectedIdentity=1
targetedNGS_expectedBaseQ=37
targetedNGS_expectedMapQ=60
targetedNGS_coverageWeight=0.25
targetedNGS_identityWeight=0.25
targetedNGS_baseqWeight=0.25
targetedNGS_mapqWeight=0.25

[PiReT transcriptomics analysis]
DoPiReTAnalysis=0
piret_input_dir=
piret_exp_design_file=
piret_kingdom=prokarya
piret_prokaryote_fasta=
piret_prokaryote_gff=
piret_eukarya_fasta=
piret_eukarya_gff=
piret_p_value=0.001
piret_method=DEedge
piret_stranded=0
piret_index=

[Generate JBrowse Tracks]
DoJBrowse=1

[HTML Report]
DoHTMLReport=1