Assemble mitochondrial genomes from short read data: Difference between revisions
(Created page with "-------------------------------------------------------------- <source lang='bash'> #!/bin/bash #SBATCH --time=10000 #SBATCH --mem=16000 #SBATCH --ntasks=8 #SBATCH --nodes=1 ...") |
No edit summary |
||
| Line 1: | Line 1: | ||
<source lang='bash'> | <source lang='bash'> | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --time= | #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= | #SBATCH --output=output_%j.txt | ||
#SBATCH --error= | #SBATCH --error=error_output_%j.txt | ||
#SBATCH --job-name= | #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 | |||
Revision as of 13:09, 26 March 2014
<source lang='bash'>
- !/bin/bash
- SBATCH --time=1000
- SBATCH --mem=16000
- SBATCH --ntasks=8
- SBATCH --nodes=1
- SBATCH --constraint=normalmem
- SBATCH --output=output_%j.txt
- SBATCH --error=error_output_%j.txt
- SBATCH --job-name=assemble_mito
- SBATCH --partition=ABGC_Research
- SBATCH --mail-type=ALL
- 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 | 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>
<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