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settings.sample.ini
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settings.sample.ini
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iniVersion = 5
[Files]
# Fasta sequences obtain from the next generation sequencing machine
# EXAMPLE file: data.fna
# ====================================================================
fastaSequences = data.fna # see settings.ini in the EXAMPLE folder for example
# tags for identification of individuals and locus
# EXAMPLE file: tags.csv
# ================================================
tags = tags.csv # see settings.ini in the EXAMPLE folder for example
# Tag size (number of nucleotides per tag)
tagSize = 6
[Files.Alleles]
# Alleles
# =======
# List of N files, N being the number of loci
# VERY IMPORTANT:
# 1/ loci should be in the same order in the tags and allele files: e.g. if column 2 and 3 of the tags file contain tags of locus 1, 0= alleles_locus1.fas
# 2/ there must be as many fasta sequences as described alleles
# 3/ if no described alleles: an empty file should be present
0 = alleles_locus1.fas # see settings.ini in the EXAMPLE folder for example
1 = alleles_locus2.fas
2 = alleles_locus3.fas
3 = alleles_locus4.fas
[Primers]
# Primers
# =======
# List of 2N primers, N being the number of loci
# VERY IMPORTANT:
# 1/ primers should be in the same order in the tags and allele files: e.g. if column 2 and 3 of the tags file contain tags of locus 1 and if in Alleles 0= # alleles_locus1.fas, 0= forward primer of locus 1 and 1 = reverse primer of locus 1
# 2/ you can either use the complete sequence of the primer (e.g. 0 and 1) or only the first x-bp (e.g 2 and 3)
0 = GAGTGTCATTTCTCCAACsrGA # see settings.ini in the EXAMPLE folder for example
1 = TyAmCTCTCCkCTCCACAGTGAA
2 = ACG
3 = TTC
4 = AyCTCCGTGTCCCGGCCC
5 = GCAGGTTGCTCAGGCCCACTT
6 = AyCTCCGTGTCCCGGCCC
7 = GCGCAGGGTGTTCAAGCACAT
[AlleleDiscovering]
# Should reads different from previously described alleles be named?
discovering = True
# Threshold number of reads above which a variant different from a previously described alleles should be named
# if the number of reads of a given variant is less than this threshold: the reads are named as <'unidentified'>
# Here, 2 has been choosen to caracterize singletons as <'unidentified'>
threshold = 2
# Should new alleles be written in the alleles file:
# if False potential new alleles will be written in the file: alleles_locusN.fas
# if True potential new alleles will be written in the file: alleles_locusN_new.fas
toNewFiles = False
[Results]
# What to write in the result file
# 0 : write only reads for which we have identified individual, locus and previously decribed allele
# 1 : write only reads for which we have identified individual and locus
# 2 : write all
showUnidentified = 1
[AlleleDiscovering.CropLengths]
# Cut the primers from the reads
# VERY IMPORTANT:
# 1/ specify the complete length of the primers even if you use only the first x-bp
0 = 22 # see settings.ini in the EXAMPLE folder for example
1 = 23
2 = 20
3 = 23
4 = 18
5 = 21
6 = 19
7 = 21