Initial commit

.gitignore

+# exclude everything
+02-raw/*
+03-samples/* 
+04-all_samples/*
+05-stacks/*
+06-populations/*
+08-genomes/*
+10-logs/*
+# exception to the rule
+!02-raw/.gitkeep
+!03-samples/.gitkeep
+!04-all_samples/.gitkeep
+!05-stacks/.gitkeep
+!06-populations/.gitkeep
+!08-genomes/.gitkeep
+!10-logs/.gitkeep
\ No newline at end of file

00-scripts/bwa_mem_align_reads_PE.sh

+#!/bin/bash
+
+# Global variables
+GENOMEFOLDER="08-genomes"
+##prefix of the genome files
+GENOME=$1
+##path of the folder which contains demultiplexed/"clonefiltered" samples
+DATAFOLDER=$2
+## number of available CPU cores (default : 64)
+NCPU=$3
+
+
+# Test if user specified a number of CPUs
+if [[ -z "$NCPU" ]]
+then
+    NCPU=64
+fi
+# temporary results from bwa mem command
+temp_bwa=$$.temp_bwa
+
+## Index genome if not alread done
+#bwa index -p $GENOMEFOLDER/$GENOME $GENOMEFOLDER/$GENOME.fasta
+
+for file in $(ls -1 $DATAFOLDER/*.1.fq.gz)
+do
+    # Name of uncompressed file
+    file2=$(echo "$file" | sed 's/\.1\./.2./g')
+    echo "Aligning file $file $file2" 
+    name=$(basename $file)
+    name2=$(basename $file2)
+    ID="@RG\tID:ind\tSM:ind\tPL:Illumina"
+
+    # Align reads 1 step
+    bwa mem -t "$NCPU" -R "$ID" $GENOMEFOLDER/$GENOME $DATAFOLDER/"$name" $DATAFOLDER/"$name2" 2> /dev/null > $temp_bwa
+    samtools view -Sb -q 20 $temp_bwa > $DATAFOLDER/"${name%.1.fq.gz}".bam
+    #samtools view -Sb -q 20 -f 83 -f 163 -f 99 -f 147 - > $DATAFOLDER/"${name%.fq.gz}".bam
+    # Sort and index
+    samtools sort $DATAFOLDER/"${name%.1.fq.gz}".bam  -o $DATAFOLDER/"${name%.1.fq.gz}".sorted.bam
+    samtools index $DATAFOLDER/"${name%.1.fq.gz}".sorted.bam
+    rm $temp_bwa
+done

00-scripts/rename_files.sh

+## rename files
+#argument 1 : path of the results 04-all_samples/species
+#argument 2 : path of the infos files 01-info_files/species_infos.csv
+mkdir $1
+awk -F, '{ print $1"\t"$2"\t"$3"\t"$4}' $2 | while read NUMB RUN BARCODE NAME_IND ;
+do
+ FOLDER_RUN=`ls $(pwd)/03-samples/$NUMB/ | grep $RUN | grep clone`
+ FILE_R1=`ls $(pwd)/03-samples/$NUMB/$FOLDER_RUN/ | grep $BARCODE | grep ".1.1."`
+ FILE_R2=`ls $(pwd)/03-samples/$NUMB/$FOLDER_RUN/ | grep $BARCODE | grep ".2.2."`
+ if [ -z "$FILE_R1" ]
+ then
+  echo "\$var is empty"
+ else
+  PATH_R1=$(pwd)/03-samples/$NUMB/$FOLDER_RUN/$FILE_R1
+  PATH_R2=$(pwd)/03-samples/$NUMB/$FOLDER_RUN/$FILE_R2
+  echo $PATH_R1 $PATH_R2
+  ln -s $PATH_R1 $1/$NAME_IND".1.fq.gz"
+  ln -s $PATH_R2 $1/$NAME_IND".2.fq.gz"
+ fi
+done

00-scripts/step1.sf

+configfile: "01-info_files/config.yaml"
+
+RUNPOOLS, POOLS = glob_wildcards('02-raw/{runpool}/{pool}_R1_001.fastq.gz')
+
+rule all:
+    input:
+        directory(expand('03-samples/{runpool}', runpool=RUNPOOLS)),        
+        directory(expand('03-samples/{runpool}_clone_filtered', runpool=RUNPOOLS)),
+        expand('10-logs/process_radtags/{runpool}.log',runpool=RUNPOOLS),
+        expand('10-logs/clone_filter/{runpool}.log',runpool=RUNPOOLS)
+
+### demultiplexing
+rule process_radtags:
+    input:
+        '02-raw/{runpool}/'
+    output:
+        directory('03-samples/{runpool}')
+    params:
+        enzyme=config["process_radtags"]["enzyme"],
+        trim_length=config["process_radtags"]["trim_length"],
+        score_limit=config["process_radtags"]["score_limit"],
+        encoded=config["process_radtags"]["encoded"],
+        barcode_dist_1=config["process_radtags"]["barcode_dist_1"]
+        barcode_dist_2=config["process_radtags"]["barcode_dist_2"]
+    log:
+        '10-logs/process_radtags/{runpool}.log'
+    shell:
+        '''mkdir -p {output};
+        process_radtags -i gzfastq -P -p {input} -o {output} -b 01-info_files/barcodes.txt -c -r -t {params.trim_length} --barcode_dist_1 {params.barcode_dist_1} --barcode_dist_2 {params.barcode_dist_2} -s {params.score_limit} -E {params.encoded} -e {params.enzyme} 2> {log}'''
+
+### clone filter
+rule clone_filter:
+    input:
+        directory('03-samples/{runpool}')
+    output:
+        directory('03-samples/{runpool}_clone_filtered')
+    log:
+        '10-logs/clone_filter/{runpool}.log'
+    shell:
+        '''mkdir -p {output};
+        for p in `ls {input}/*fq.gz | grep -v *rem* | cut -d "." -f 1 | sort | uniq`;
+        do clone_filter -1 "$p".1.fq.gz -2 "$p".2.fq.gz -i gzfastq -o {output} 2> {log};
+        done'''

00-scripts/step2.sf

+configfile: "01-info_files/config.yaml"
+
+rule all:
+    input:
+        expand('08-genomes/{species}_genome.fasta',species=config["species"]),
+        expand('10-logs/index_genome/{species}.log',species=config["species"])
+
+
+### index genome
+rule index_genome:
+    input:
+        fasta='08-genomes/{species}_genome.fasta'
+    params:
+        '08-genomes/{species}_genome'
+    log:
+        '10-logs/index_genome/{species}.log'
+    shell:
+        '''bwa index -p {params} {input.fasta} 2> {log}'''
+                                                      
\ No newline at end of file

00-scripts/step3.sf

+configfile: "01-info_files/config.yaml"
+
+rule all:
+    input:
+        directory(expand('04-all_samples/{species}',species=config["species"])),
+        expand('01-info_files/{species}_infos.csv',species=config["species"]),
+        expand('10-logs/genome_alignment/{species}.log',species=config["species"])
+
+### rename file
+rule rename_file:
+    input:        
+        infos='01-info_files/{species}_infos.csv'
+    output:
+        directory('04-all_samples/{species}')
+    shell:
+        '''bash ./00-scripts/rename_files.sh {output} {input.infos}'''
+
+### genome alignment
+rule genome_alignment:
+    input:
+        ancient(directory('04-all_samples/{species}'))
+    threads: config["genome_alignment"]["cores_bwa"]
+    params:
+        '{species}_genome'
+    output:
+        '10-logs/genome_alignment/{species}.log'
+    shell:
+        '''bash ./00-scripts/bwa_mem_align_reads_PE.sh {params} {input} {threads} 2> {output}'''

00-scripts/step4.sf

+configfile: "01-info_files/config.yaml"
+
+rule all:
+    input:
+        directory(expand('04-all_samples/{species}',species=config["species"])),
+        directory(expand('05-stacks/{species}',species=config["species"])),
+        expand('01-info_files/{species}_population_map.txt',species=config["species"]),
+        directory(expand('06-populations/{species}',species=config["species"])),
+        expand('10-logs/gstacks/{species}.log',species=config["species"]),
+        expand('10-logs/populations/{species}.log',species=config["species"])
+
+if config["population_map"] != "n":
+    ### population map
+    rule population_map:
+        input:
+            directory('04-all_samples/{species}')
+        output:
+            popMap='01-info_files/{species}_population_map.txt'            
+        shell:
+             '''for i in `ls {input} | grep ".sorted.bam.bai"`;
+          do namef=`echo $i | cut -d "." -f 1-2`;
+          popID=`echo $i | cut -d "_" -f 2` ;
+          printf $namef"\t"$popID"\n";
+          done | sort | uniq > {output.popMap};
+          mkdir {output.stacksDir};'''
+
+
+### gstacks
+rule run_gstacks:
+    input:
+        sdir=directory('04-all_samples/{species}'),
+        popm='01-info_files/{species}_population_map.txt'
+    output:
+        directory('05-stacks/{species}')
+    threads: config["gstacks"]["cores"]
+    log:
+        '10-logs/gstacks/{species}.log'
+    shell:
+        '''mkdir -p {output};
+        gstacks -I {input.sdir} -t {threads} -M {input.popm} -O {output} > {log}'''
+
+
+### populations
+rule run_populations:
+    input:
+        gdir=directory('05-stacks/{species}'),
+        popm='01-info_files/{species}_population_map.txt'
+    output:
+        directory('06-populations/{species}')
+    threads: config["populations"]["cores"]
+    params:
+        r=config["populations"]["r"],
+        p=config["populations"]["p"],
+        f=config["populations"]["f"],
+        a=config["populations"]["a"],
+        p_value_cutoff=config["populations"]["p_value_cutoff"],
+        lnl_lim=config["populations"]["lnl_lim"]
+    log:
+        '10-logs/populations/{species}.log'
+    shell:
+        '''mkdir -p {output};
+        populations -t {threads} -P {input.gdir} -M {input.popm} -r {params.r} -p {params.p} -f {params.f} -a {params.a} --p_value_cutoff {params.p_value_cutoff} --lnl_lim {params.lnl_lim} --write_single_snp --vcf --vcf_haplotypes --structure -O {output} > {log}'''

01-info_files/barcodes.txt

+AAACGG
+AACGTT
+AACTGA
+AAGACG
+AAGCTA
+AATATC
+AATGAG
+ACAAGA
+ACAGCG
+ACATAC
+ACCATG
+ACCCCC
+ACTCTT
+ACTGGC
+AGCCAT
+AGCGCA
+AGGGTC
+AGGTGT
+AGTAGG
+AGTTAA
+ATAGTA
+ATCAAA
+ATGCAC
+ATGTTG
+ATTCCG
+CAAAAA
+CAATCG
+CACCTC
+CAGGCA
+CATACT
+CCATTT
+CCCGGT
+CCCTAA
+CCGAGG
+CCGCAT
+CCTAAC
+CGAGGC
+CGCAGA
+CGCGTG
+CGGTCC
+CGTCTA
+CGTGAT
+CTACAG
+CTCGCC
+CTGCGA
+CTGGTT
+CTTATG
+CTTTGC

01-info_files/config.yaml

+process_radtags:
+    enzyme : SbfI
+    trim_length : 143
+    score_limit : 20
+    encoded : phred33
+    barcode_dist_1 : 2
+    barcode_dist_2 : 2
+species:
+ - mullus
+ - serran
+ - diplodus
+genome_alignment:
+    cores_bwa : 32
+population_map: n
+gstacks:
+    cores : 32
+populations:
+    cores : 32
+    r : 0.85
+    p : 1
+    f : p_value
+    a : 0.05
+    p_value_cutoff : 0.10
+    lnl_lim : -10
+

01-info_files/diplodus_infos.csv

+2,H23244,AGCCAT,dip_spaAL_070
+2,H23244,AGCGCA,dip_spaN_002
+2,H23244,AGGGTC,dip_bal_077
+2,H23244,AGGTGT,dip_spaS_078
+2,H23244,AGTAGG,dip_spaS_036
+2,H23244,AGTTAA,dip_fra_031
+2,H23244,ATAGTA,dip_bal_054
+2,H23244,ATCAAA,dip_fra_039
+2,H23244,ATGCAC,dip_bal_113
+2,H23244,ATGTTG,dip_spaN_019
+2,H23244,ATTCCG,dip_spaAL_040
+2,H23244,CAAAAA,dip_spaS_031
+2,H23244,CAATCG,dip_bal_102
+2,H23244,CACCTC,dip_spaS_079
+2,H23244,CAGGCA,dip_spaAL_051
+2,H23244,CATACT,dip_spaAL_049
+2,H23244,CCATTT,dip_spaAL_024
+2,H23244,CCCGGT,dip_fra_059
+2,H23244,CCCTAA,dip_spaAL_079
+2,H23244,CCGAGG,dip_fra_028
+2,H23244,CCGCAT,dip_bal_071
+2,H23244,CCTAAC,dip_bal_108
+2,H23244,CGAGGC,dip_spaAL_067
+2,H23244,CGCAGA,dip_spaS_093
+2,H23244,CGCGTG,dip_spaAL_026
+2,H23244,CGGTCC,dip_spaS_054
+2,H23244,CGTCTA,dip_spaS_029
+2,H23244,CGTGAT,dip_bal_031
+2,H23244,CTACAG,dip_fra_036
+2,H23244,CTCGCC,dip_spaS_114
+2,H23244,CTGCGA,dip_spaAL_008
+2,H23244,CTGGTT,dip_spaS_020
+2,H23244,CTTATG,dip_spaN_080
+2,H23244,CTTTGC,dip_fra_076
+2,H23292,AAACGG,dip_bal_118
+2,H23292,AACGTT,dip_spaAL_022
+2,H23292,AACTGA,dip_spaS_102
+2,H23292,AAGACG,dip_spaS_080
+2,H23292,AAGCTA,dip_bal_120
+2,H23292,AATATC,dip_bal_027
+2,H23292,AATGAG,dip_spaS_043
+2,H23292,ACAAGA,dip_fra_043
+2,H23292,ACAGCG,dip_bal_014
+2,H23292,ACATAC,dip_bal_107
+2,H23292,ACCATG,dip_bal_105
+2,H23292,ACCCCC,dip_bal_109
+2,H23292,ACTCTT,dip_spaS_008
+2,H23292,ACTGGC,dip_bal_067
+2,H23292,AGCCAT,dip_spaAL_075
+2,H23292,AGCGCA,dip_fra_094
+2,H23292,AGGGTC,dip_bal_037
+2,H23292,AGGTGT,dip_spaAL_069
+2,H23292,AGTAGG,dip_spaN_001
+2,H23292,AGTTAA,dip_fra_051
+2,H23292,ATAGTA,dip_spaS_064
+2,H23292,ATCAAA,dip_fra_005
+2,H23292,ATGCAC,dip_fra_100
+2,H23292,ATGTTG,dip_spaS_025
+2,H23292,ATTCCG,dip_fra_023
+2,H23292,CAAAAA,dip_fra_046
+2,H23292,CAATCG,dip_spaAL_023
+2,H23292,CACCTC,dip_spaAL_028
+2,H23292,CAGGCA,dip_spaN_004
+2,H23292,CATACT,dip_spaN_035
+2,H23292,CCATTT,dip_bal_016
+2,H23292,CCCGGT,dip_spaS_094
+2,H23292,CCCTAA,dip_bal_003
+2,H23292,CCGAGG,dip_spaS_013
+2,H23292,CCGCAT,dip_spaAL_011
+2,H23292,CCTAAC,dip_fra_056
+2,H23292,CGAGGC,dip_spaN_012
+2,H23292,CGCAGA,dip_bal_115
+2,H23292,CGCGTG,dip_fra_095
+2,H23292,CGGTCC,dip_bal_030
+2,H23292,CGTCTA,dip_fra_049
+2,H23292,CGTGAT,dip_bal_094
+2,H23292,CTACAG,dip_bal_002
+2,H23292,CTCGCC,dip_spaS_001
+2,H23292,CTGCGA,dip_fra_061
+2,H23292,CTGGTT,dip_spaS_111
+2,H23292,CTTATG,dip_spaS_101
+2,H23292,CTTTGC,dip_spaAL_020
+2,H23340,AAACGG,dip_spaS_116
+2,H23340,AACGTT,dip_spaN_072
+2,H23340,AACTGA,dip_spaAL_068
+2,H23340,AAGACG,dip_bal_029
+2,H23340,AAGCTA,dip_bal_074
+2,H23340,AATATC,dip_spaS_078
+2,H23340,AATGAG,dip_fra_042
+2,H23340,ACAAGA,dip_fra_070
+2,H23340,ACAGCG,dip_fra_088
+2,H23340,ACATAC,dip_fra_001
+2,H23340,ACCATG,dip_spaAL_076
+2,H23340,ACCCCC,dip_spaN_003
+2,H23340,ACTCTT,dip_spaN_020
+2,H23340,ACTGGC,dip_fra_011
+2,H23340,AGCCAT,dip_spaS_110
+2,H23340,AGCGCA,dip_fra_098
+2,H23340,AGGGTC,dip_fra_044
+2,H23340,AGGTGT,dip_fra_041
+2,H23340,AGTAGG,dip_fra_060
+2,H23340,AGTTAA,dip_bal_078
+2,H23340,ATAGTA,dip_fra_082
+2,H23340,ATCAAA,dip_bal_017
+2,H23340,ATGCAC,dip_spaN_046
+2,H23340,ATGTTG,dip_fra_062
+2,H23340,ATTCCG,dip_fra_057
+2,H23340,CAAAAA,dip_fra_089
+2,H23340,CAATCG,dip_bal_103
+2,H23340,CACCTC,dip_spaS_004
+2,H23340,CAGGCA,dip_fra_037
+2,H23340,CATACT,dip_fra_093
+2,H23340,CCATTT,dip_spaAL_084
+2,H23340,CCCGGT,dip_fra_090
+2,H23340,CCCTAA,dip_bal_083
+2,H23340,CCGAGG,dip_spaN_036
+2,H23340,CCGCAT,dip_bal_019
+2,H23340,CCTAAC,dip_spaS_050
+2,H23340,CGAGGC,dip_fra_040
+2,H23340,CGCAGA,dip_bal_082
+2,H23340,CGCGTG,dip_bal_119
+2,H23340,CGGTCC,dip_spaS_005
+2,H23340,CGTCTA,dip_bal_050
+2,H23340,CGTGAT,dip_spaN_057
+2,H23340,CTACAG,dip_fra_087
+2,H23340,CTCGCC,dip_bal_089
+2,H23340,CTGCGA,dip_fra_021
+2,H23340,CTGGTT,dip_bal_072
+2,H23340,CTTATG,dip_bal_095
+2,H23340,CTTTGC,dip_spaAL_035
+2,H23388,AAACGG,dip_fra_066
+2,H23388,AACGTT,dip_spaS_096
+2,H23388,AACTGA,dip_bal_025
+2,H23388,AAGACG,dip_spaS_012
+2,H23388,AAGCTA,dip_fra_084
+2,H23388,AATATC,dip_bal_091
+2,H23388,AATGAG,dip_fra_096
+2,H23388,ACAAGA,dip_fra_009
+2,H23388,ACAGCG,dip_fra_022
+2,H23388,ACATAC,dip_bal_001
+2,H23388,ACCATG,dip_spaAL_042
+2,H23388,ACCCCC,dip_spaS_023
+2,H23388,ACTCTT,dip_fra_047
+2,H23388,ACTGGC,dip_spaS_112
+2,H23388,AGCCAT,dip_bal_060
+2,H23388,AGCGCA,dip_fra_071
+2,H23388,AGGGTC,dip_spaS_097
+2,H23388,AGGTGT,dip_fra_079
+2,H23388,AGTAGG,dip_bal_079
+2,H23388,AGTTAA,dip_spaAL_047
+2,H23388,ATAGTA,dip_fra_050
+2,H23388,ATCAAA,dip_spaAL_057
+2,H23388,ATGCAC,dip_fra_058
+2,H23388,ATGTTG,dip_fra_052
+2,H23388,ATTCCG,dip_fra_077
+2,H23388,CAAAAA,dip_fra_034
+2,H23388,CAATCG,dip_bal_020
+2,H23388,CACCTC,dip_fra_068
+2,H23388,CAGGCA,dip_bal_110
+2,H23388,CATACT,dip_spaS_081
+2,H23388,CCATTT,dip_fra_078
+2,H23388,CCCGGT,dip_fra_081
+2,H23388,CCCTAA,dip_fra_054
+2,H23388,CCGAGG,dip_bal_116
+2,H23388,CCGCAT,dip_spaN_071
+2,H23388,CCTAAC,dip_fra_080
+2,H23388,CGAGGC,dip_spaS_119
+2,H23388,CGCAGA,dip_spaN_016
+2,H23388,CGCGTG,dip_bal_062
+2,H23388,CGGTCC,dip_spaS_069
+2,H23388,CGTCTA,dip_spaAL_077
+2,H23388,CGTGAT,dip_spaS_070
+2,H23388,CTACAG,dip_spaAL_063
+2,H23388,CTCGCC,dip_spaS_117
+2,H23388,CTGCGA,dip_fra_063
+2,H23388,CTGGTT,dip_bal_005
+2,H23388,CTTATG,dip_bal_080
+2,H23388,CTTTGC,dip_fra_045
+2,H23436,AAACGG,dip_fra_099
+2,H23436,AACGTT,dip_bal_065
+2,H23436,AACTGA,dip_bal_114
+2,H23436,AAGACG,dip_spaN_006
+2,H23436,AAGCTA,dip_bal_096
+2,H23436,AATATC,dip_bal_056
+2,H23436,AATGAG,dip_bal_024
+2,H23436,ACAAGA,dip_spaAL_066
+2,H23436,ACAGCG,dip_fra_035
+2,H23436,ACATAC,dip_fra_007
+2,H23436,ACCATG,dip_spaN_010
+2,H23436,ACCCCC,dip_bal_048
+2,H23436,ACTCTT,dip_spaN_062
+2,H23436,ACTGGC,dip_bal_022
+2,H23436,AGCCAT,dip_spaN_009
+2,H23436,AGCGCA,dip_spaN_008
+2,H23436,AGGGTC,dip_fra_091
+2,H23436,AGGTGT,dip_spaS_018
+2,H23436,AGTAGG,dip_bal_112
+2,H23436,AGTTAA,dip_spaN_011
+2,H23436,ATAGTA,dip_bal_010
+2,H23436,ATCAAA,dip_spaAL_062
+2,H23436,ATGCAC,dip_fra_072
+2,H23436,ATGTTG,dip_spaAL_037
+2,H23436,ATTCCG,dip_fra_053
+2,H23436,CAAAAA,dip_spaAL_081
+2,H23436,CAATCG,dip_bal_101
+2,H23436,CACCTC,dip_spaS_059
+2,H23436,CAGGCA,dip_bal_099
+2,H23436,CATACT,dip_spaS_030
+2,H23436,CCATTT,dip_spaN_017
+2,H23436,CCCGGT,dip_bal_013
+2,H23436,CCCTAA,dip_fra_029
+2,H23436,CCGAGG,dip_spaS_113
+2,H23436,CCGCAT,dip_spaS_037
+2,H23436,CCTAAC,dip_spaS_011
+2,H23436,CGAGGC,dip_fra_048
+2,H23436,CGCAGA,dip_spaS_053
+2,H23436,CGCGTG,dip_spaAL_060
+2,H23436,CGGTCC,dip_fra_085
+2,H23436,CGTCTA,dip_fra_024
+2,H23436,CGTGAT,dip_fra_073
+2,H23436,CTACAG,dip_spaAL_015
+2,H23436,CTCGCC,dip_fra_038
+2,H23436,CTGCGA,dip_bal_061
+2,H23436,CTGGTT,dip_spaAL_044
+2,H23436,CTTATG,dip_bal_009
+2,H23436,CTTTGC,dip_spaS_060
+2,H23484,AAACGG,dip_fra_083
+2,H23484,AACGTT,dip_spaAL_058
+2,H23484,AACTGA,dip_bal_018
+2,H23484,AAGACG,dip_fra_032
+2,H23484,AAGCTA,dip_bal_100
+2,H23484,AATATC,dip_bal_053
+2,H23484,AATGAG,dip_bal_097
+2,H23484,ACAAGA,dip_bal_006
+2,H23484,ACAGCG,dip_bal_084
+2,H23484,ACATAC,dip_spaS_118
+2,H23484,ACCATG,dip_bal_111
+2,H23484,ACCCCC,dip_bal_004
+2,H23484,ACTCTT,dip_bal_028
+2,H23484,ACTGGC,dip_fra_033
+2,H23484,AGCCAT,dip_spaAL_074
+2,H23484,AGCGCA,dip_spaAL_031
+2,H23484,AGGGTC,dip_spaAL_064
+2,H23484,AGGTGT,dip_fra_026
+2,H23484,AGTAGG,dip_spaS_095
+2,H23484,AGTTAA,dip_spaAL_006
+2,H23484,ATAGTA,dip_fra_002
+2,H23484,ATCAAA,dip_spaN_015
+2,H23484,ATGCAC,dip_spaS_045
+2,H23484,ATGTTG,dip_bal_015
+2,H23484,ATTCCG,dip_spaAL_061
+2,H23484,CAAAAA,dip_fra_030
+2,H23484,CAATCG,dip_bal_021
+2,H23484,CACCTC,dip_spaAL_083
+2,H23484,CAGGCA,dip_spaS_115
+2,H23484,CATACT,dip_spaN_047
+2,H23484,CCATTT,dip_spaAL_078
+2,H23484,CCCGGT,dip_spaS_035
+2,H23484,CCCTAA,dip_spaS_082
+2,H23484,CCGAGG,dip_fra_065
+2,H23484,CCGCAT,dip_spaN_021
+2,H23484,CCTAAC,dip_bal_081
+2,H23484,CGAGGC,dip_spaAL_003
+2,H23484,CGCAGA,dip_bal_073
+2,H23484,CGCGTG,dip_fra_014
+2,H23484,CGGTCC,dip_spaAL_065
+2,H23484,CGTCTA,dip_spaS_100
+2,H23484,CGTGAT,dip_bal_012
+2,H23484,CTACAG,dip_bal_045
+2,H23484,CTCGCC,dip_bal_085
+2,H23484,CTGCGA,dip_fra_097
+2,H23484,CTGGTT,dip_fra_025
+2,H23484,CTTATG,dip_fra_012
+2,H23484,CTTTGC,dip_spaAL_059
+2,H23532,AAACGG,dip_fra_069
+2,H23532,AACGTT,dip_spaN_013
+2,H23532,AACTGA,dip_spaN_005
+2,H23532,AAGACG,dip_spaS_027
+2,H23532,AAGCTA,dip_fra_055
+2,H23532,AATATC,dip_bal_117
+2,H23532,AATGAG,dip_bal_086
+2,H23532,ACAAGA,dip_spaAL_016
+2,H23532,ACAGCG,dip_spaS_041
+2,H23532,ACATAC,dip_spaN_014
+2,H23532,ACCATG,dip_bal_063
+2,H23532,ACCCCC,dip_bal_098
+2,H23532,ACTCTT,dip_fra_003
+2,H23532,ACTGGC,dip_spaS_068
+2,H23532,AGCCAT,dip_fra_064
+2,H23532,AGCGCA,dip_spaAL_055
+2,H23532,AGGGTC,dip_bal_026
+2,H23532,AGGTGT,dip_spaN_054
+2,H23532,AGTAGG,dip_spaN_007
+2,H23532,AGTTAA,dip_bal_007
+2,H23532,ATAGTA,dip_bal_011
+2,H23532,ATCAAA,dip_bal_023
+2,H23532,ATGCAC,dip_bal_087
+2,H23532,ATGTTG,dip_fra_086
+2,H23532,ATTCCG,dip_fra_027

01-info_files/diplodus_population_map.txt

+dip_bal_001.sorted	bal
+dip_bal_002.sorted	bal
+dip_bal_003.sorted	bal
+dip_bal_004.sorted	bal
+dip_bal_005.sorted	bal
+dip_bal_006.sorted	bal
+dip_bal_007.sorted	bal
+dip_bal_009.sorted	bal
+dip_bal_010.sorted	bal
+dip_bal_011.sorted	bal
+dip_bal_012.sorted	bal
+dip_bal_013.sorted	bal
+dip_bal_014.sorted	bal
+dip_bal_015.sorted	bal
+dip_bal_016.sorted	bal
+dip_bal_017.sorted	bal
+dip_bal_018.sorted	bal
+dip_bal_019.sorted	bal
+dip_bal_020.sorted	bal
+dip_bal_021.sorted	bal
+dip_bal_022.sorted	bal
+dip_bal_023.sorted	bal
+dip_bal_024.sorted	bal