mitoz scripts

.gitignore

+mitoZ/extractfq
+mitoZ/MitoZ.simg

mitoZ/INSTALL.sh

+###############################################################################
+## MitoZ
+## mitoz singularuty img
+sudo singularity pull --name MitoZ.simg shub://linzhi2013/MitoZ:v2.3
+## extract fastq seq python3 script
+git clone https://github.com/linzhi2013/extractfq.git
+
+

mitoZ/extractfq.sh

+EXTRACT_FQ_SEQ=`echo "python3 //media/bigvol/peguerin/extractfq/extractfq/extractfq.py"`
+## data files
+RAWFQGZ1="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
+RAWFQGZ2="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
+
+
+##extract 5 Go
+mkdir 02-raw
+$EXTRACT_FQ_SEQ -fq1 $RAWFQGZ1 -fq2 $RAWFQGZ2 -outfq1 02-raw/raw.1.fq -outfq2 02-raw/raw.2.fq -size_required 5

mitoZ/mitoz_all.sh

+## softwares/scripts
+MITOZ="/media/bigvol/peguerin/MitoZ.simg"
+## data files
+RAWFQGZ1="02-raw/raw.1.fq"
+RAWFQGZ2="02-raw/raw.2.fq"
+
+
+$MITOZ  all --genetic_code 2 --clade Chordata --outprefix mito_mullus \
+--thread_number 64 \
+--fastq1 $RAWFQGZ1 \
+--fastq2 $RAWFQGZ2 \
+--fastq_read_length 150 \
+--insert_size 350  \
+--run_mode 2 \
+--filter_taxa_method 1 \
+--requiring_taxa 'Chordata'

mitoZ/script.sh

+## softwares/scripts
+MITOZ="/home/pguerin/working/intrapop/projets/assemble_mitogenome/MitoZ.simg"
+EXTRACT_FQ_SEQ=`echo "python3 /home/pguerin/working/intrapop/projets/assemble_mitogenome/extractfq/extractfq/extractfq.py"`
+## data files
+RAWFQGZ1="/donnees/RESERVEBENEFIT/whole_genome_sequencing/wgs_mullus/JFP-1-2_pairedend/data/fasteris/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
+RAWFQGZ2="/donnees/RESERVEBENEFIT/whole_genome_sequencing/wgs_mullus/JFP-1-2_pairedend/data/fasteris/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
+
+$MITOZ all --create_config
+
+##extract 5 Go
+mkdir 02-raw
+$EXTRACT_FQ_SEQ -fq1 $RAWFQGZ1 -fq2 $RAWFQGZ2 -outfq1 02-raw/raw.1.fq -outfq2 02-raw/raw.2.fq -size_required 5
+
+
+$MITOZ  all --genetic_code 2 --clade Chordata --outprefix mito_mullus \
+--thread_number 8 \
+--fastq1 02-raw/raw.1.fq \
+--fastq2 02-raw/raw.2.fq \
+--fastq_read_length 150 \
+--insert_size 250  \
+--run_mode 2 \
+--filter_taxa_method 1 \
+--requiring_taxa 'Chordata'
+
+
+/media/bigvol/peguerin
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