Assemble mitochondrial genomes from short read data - Revision history

Dawes0011 at 08:58, 16 June 2023

2023-06-16T08:58:46Z

← Older revision		Revision as of 10:58, 16 June 2023
Line 33:		Line 33:
	bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| awk '$5>0' \| head -10000 >>$1_mito_align.sam		bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| awk '$5>0' \| head -10000 >>$1_mito_align.sam

	java7 -jar ~~/cm~~/shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True		java7 -jar /shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True

	SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo.config -o $1_mito_assembly.fa		SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo.config -o $1_mito_assembly.fa

Dawes001 at 15:00, 15 July 2019

2019-07-15T15:00:46Z

← Older revision		Revision as of 17:00, 15 July 2019
Line 22:		Line 22:
	#SBATCH --ntasks=8		#SBATCH --ntasks=8
	#SBATCH --nodes=1		#SBATCH --nodes=1
	#SBATCH --constraint=~~normalmem~~		#SBATCH --constraint=4gpercpu
	#SBATCH --output=output_%j.txt		#SBATCH --output=output_%j.txt
	#SBATCH --error=error_output_%j.txt		#SBATCH --error=error_output_%j.txt
	#SBATCH --job-name=assemble_mito		#SBATCH --job-name=assemble_mito
	~~#SBATCH --partition=ABGC_Research~~
	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL
	#SBATCH --mail-user=hendrik-jan.megens@wur.nl		#SBATCH --mail-user=hendrik-jan.megens@wur.nl

Megen002 at 12:19, 26 March 2014

2014-03-26T12:19:51Z

← Older revision		Revision as of 14:19, 26 March 2014
Line 44:		Line 44:
	</source>		</source>

			Invoke like this:
	<source lang='bash'>		<source lang='bash'>
	sh do_mtalign_bowtie_pig.sh MA01F18 33\		sbatch do_mtalign_bowtie_pig.sh MA01F18 33\
	/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz\		/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz\
	/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz		/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz

Megen002 at 12:18, 26 March 2014

2014-03-26T12:18:54Z

← Older revision		Revision as of 14:18, 26 March 2014
Line 45:		Line 45:

	<source lang='bash'>		<source lang='bash'>
	sh do_mtalign_bowtie_pig.sh MA01F18 33 /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz		sh do_mtalign_bowtie_pig.sh MA01F18 33\
			/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz\
			/lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz

Megen002 at 12:18, 26 March 2014

2014-03-26T12:18:09Z

@@ Line 1: / Line 1: @@
-A simple procedure for assembling mitochondrial genomes based on whole-genome re-sequencing data. The first step is to extract reads from the sequence library based on a closely related entirely assembled genome (e.g., for pig, the MT genome as present in the genome build, but could also be of a related species). The genome is then assembled using
+A simple procedure for assembling mitochondrial genomes based on whole-genome re-sequencing data. The first step is to extract reads from the sequence library based on a closely related entirely assembled genome (e.g., for pig, the MT genome as present in the genome build, but could also be of a related species). The genome is then assembled using SOAPdenovo.
 <source lang='bash'>
@@ Line 21: / Line 36: @@
 java7 -jar /cm/shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True
-SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo_pig.config -o $1_mito_assembly.fa
+SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo.config -o $1_mito_assembly.fa
 blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6

Megen002 at 12:14, 26 March 2014

2014-03-26T12:14:00Z

← Older revision		Revision as of 14:14, 26 March 2014
Line 1:		Line 1:
			A simple procedure for assembling mitochondrial genomes based on whole-genome re-sequencing data. The first step is to extract reads from the sequence library based on a closely related entirely assembled genome (e.g., for pig, the MT genome as present in the genome build, but could also be of a related species). The genome is then assembled using

	<source lang='bash'>		<source lang='bash'>
Line 14:		Line 14:
	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL
	#SBATCH --mail-user=hendrik-jan.megens@wur.nl		#SBATCH --mail-user=hendrik-jan.megens@wur.nl
	module load bowtie/2-2.2.1 SOAPdenovo2/r240 BLAST+/2.2.28		module load bowtie/2-2.2.1 SOAPdenovo2/r240 BLAST+/2.2.28 MUMmer/3.23

	bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| head -2 >$1_mito_align.sam		bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| head -2 >$1_mito_align.sam
Line 24:		Line 24:

	blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6		blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6

			mummer -mum -b -c mt_pig.fa $1_mito_assembly.fa.scafSeq > mummer.mums
			mummerplot -postscript -p mummer mummer.mums
	</source>		</source>

	<source lang='bash'>		<source lang='bash'>
	sh do_mtalign_bowtie_pig.sh MA01F18 33 /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz		sh do_mtalign_bowtie_pig.sh MA01F18 33 /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz

Megen002 at 12:09, 26 March 2014

2014-03-26T12:09:15Z

← Older revision		Revision as of 14:09, 26 March 2014
Line 1:		Line 1:
	~~--------------------------------------------------------------~~

	<source lang='bash'>		<source lang='bash'>
	#!/bin/bash		#!/bin/bash
	#SBATCH --time=~~10000~~		#SBATCH --time=1000
	#SBATCH --mem=16000		#SBATCH --mem=16000
	#SBATCH --ntasks=8		#SBATCH --ntasks=8
	#SBATCH --nodes=1		#SBATCH --nodes=1
	#SBATCH --constraint=normalmem		#SBATCH --constraint=normalmem
	#SBATCH --output=~~output_pep_~~%j.txt		#SBATCH --output=output_%j.txt
	#SBATCH --error=~~error_output_pep_~~%j.txt		#SBATCH --error=error_output_%j.txt
	#SBATCH --job-name=~~blastp~~		#SBATCH --job-name=assemble_mito
	#SBATCH --partition=ABGC_Research		#SBATCH --partition=ABGC_Research
	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL
	#SBATCH --mail-user=hendrik-jan.megens@wur.nl		#SBATCH --mail-user=hendrik-jan.megens@wur.nl
			module load bowtie/2-2.2.1 SOAPdenovo2/r240 BLAST+/2.2.28

	bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| head -2 >$1_mito_align.sam		bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| head -2 >$1_mito_align.sam
	bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| awk '$5>0' \| head -10000 >>$1_mito_align.sam		bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 \| awk '$5>0' \| head -10000 >>$1_mito_align.sam

	java7 -jar /cm/shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True		java7 -jar /cm/shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True

	SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo_pig.config -o $1_mito_assembly.fa		SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo_pig.config -o $1_mito_assembly.fa

	blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6		blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6
	</source		</source>

			<source lang='bash'>
			sh do_mtalign_bowtie_pig.sh MA01F18 33 /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R1.PF.fastq.gz /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ABGSA0071/ABGSA0071_MA01F18_R2.PF.fastq.gz

Megen002: Created page with "-------------------------------------------------------------- #!/bin/bash #SBATCH --time=10000 #SBATCH --mem=16000 #SBATCH --ntasks=8 #SBATCH --nodes=1 ..."

2014-03-26T12:06:13Z

Created page with "-------------------------------------------------------------- <source lang='bash'> #!/bin/bash #SBATCH --time=10000 #SBATCH --mem=16000 #SBATCH --ntasks=8 #SBATCH --nodes=1 ..."

New page

--------------------------------------------------------------

<source lang='bash'>
#!/bin/bash
#SBATCH --time=10000
#SBATCH --mem=16000
#SBATCH --ntasks=8
#SBATCH --nodes=1
#SBATCH --constraint=normalmem
#SBATCH --output=output_pep_%j.txt
#SBATCH --error=error_output_pep_%j.txt
#SBATCH --job-name=blastp
#SBATCH --partition=ABGC_Research
#SBATCH --mail-type=ALL
#SBATCH --mail-user=hendrik-jan.megens@wur.nl
bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 | head -2 >$1_mito_align.sam
bowtie2 --phred$2 --local -p 8 -x mt_pig.fa -1 $3 -2 $4 | awk '$5>0' | head -10000 >>$1_mito_align.sam

java7 -jar /cm/shared/apps/SHARED/picard-tools/picard-tools-1.109/SamToFastq.jar I=$1_mito_align.sam F=fq1.fq F2=fq2.fq INCLUDE_NON_PF_READS=True
SOAPdenovo-63mer all -K 63 -p 4 -s soapdenovo_pig.config -o $1_mito_assembly.fa
blastn -query $1_mito_assembly.fa.scafSeq -db mt_pig.fa -outfmt 6
</source