EASYstrata/example_data/example5.config at main · QuentinRougemont/EASYstrata · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
# config file
#--- COMPULSORY MINIMAL LEVEL OF INFORMATION REQUIRED -----
genome1="/path/to/EASYstrata/example_data/Slatifolia.fa"     #full path to current genome1 assembly (haplotype1 - compressed or not)
genome2=""     #full path to current genome2 assembly (haplotype2)

haplotype1="Slatifolia"  #name1 [name of haplotype1 - will be used to rename the genome and the contigs inside the genome]
haplotype2="Slatifolia_Y"  #name2 [name of haplotype2 - will be used to rename the genome and the contigs inside the genome]

#----- optional --------
ancestral_genome="" #full path to the ancestral genome to be used whenever possible
ancestral_gff=" "   #full path to the associated gff to be used whehever possible

#---- COMPULSORY INFOS ------
#--- annotate or not #
annotate="YES"  #a string (YES/NO)? if annotation = YES then annotation of the genomes will be performed
             #else gtf and fastafiles are expected and only the paml/ds/genespace etc will be performed
RelatedProt="" #/path/to/related_protein.fa" #a full path to a set of external protein data (fasta format) for braker
fungus="NO" #YES or NO set to YES if species is a fungus

## orthoDB ###
orthoDBspecies="Viridiplantae" #one of : "Metazoa" "Vertebrata" "Viridiplantae" "Arthropoda" "Eukaryota" "Fungi" "Alveolata"
#if a species is given then it will be used for annotation (in addition to eventual RNAseq and orthProteins)

#----- optional --------
#if annotate = NO then gtf should be provided:
gtf1=""
gtf2=""

#----- optional --------
#RNASeq data ?
rnaseq="YES"   #YES/NO a string stating wether rnaseq data is available or not
RNAseqlist="/path/to/EASYstrata/example_data/rnaseq.list.example5.txt"
#OR BAM file
bamlist1="" #/full/path/to/bam.aligned_on_genome1.txt" #list of bam on genome1
bamlist2="" #/full/path/to/bam.aligned_on_genome2.txt" #list of bam on genome2


#---- COMPULSORY INFOS ------
#TE INFO:
annotateTE="YES" #YES/NO
TEdatabase="/path/to/EASYstrata/example_data/trep-db_nr_Rel-19.fasta.gz" #a full path to a custom database of species/genus species TE
#NCBI species for de-novo TE:
ncbi_species="eudicots"

#BUSCO SPECIFIC ARGUMENTS:
#busco_lineage name:
busco_lineage="viridiplantae_odb10" #see busco lineage to have the list

#option for Dn/Ds, plot, etc:
scaffold="//path/to/EASYstrata/example_data/scaffold_example5.txt" #scaffold.txt #a tab separated file providing the genome name in first column, second column the scaffold for the region of interest (X/Y chromosome, supergenes, etc) third colum a string (normal or reversed) expliciting wether the scaffold orientation should be reversed or not


#option for running interproscan at the quality checks steps (can take several days for big dataset)
interpro="NO" #YES #by default set to no