Commit 2fc2d755 authored by peguerin's avatar peguerin
Browse files

mitoz scripts

parent 031780eb
mitoZ/extractfq
mitoZ/MitoZ.simg
###############################################################################
## 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
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
## 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'
## 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
\ No newline at end of file
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