Generate ONT simulated data
squigulator is a tool for simulating nanopore raw signal data. It is under development and there could be interface changes and changes to default parameters. Read more here: https://github.com/hasindu2008/squigulator
Install a precompiled copy:
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VERSION=0.3.0
wget https://github.com/hasindu2008/squigulator/releases/download/v${VERSION}/squigulator-v${VERSION}-x86_64-linux-binaries.tar.gz
tar xf squigulator-v${VERSION}-x86_64-linux-binaries.tar.gz && cd squigulator-v${VERSION}
./squigulator --help |
Location: /work/GRC_collaborations/EBV/tools/squigulator-v0.3.0
PHASE 1: No mutations introduced to reference genomes prior simulation of ONT data.
Genomes:
GRCh38.p14
EBV_ASM240226v1
GRCh38+EBV_ASM240226v1 (integrated in the genome)
GRCh38.p14 ONT simulated data:
Location:
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/work/GRC_collaborations/EBV/analysis/1.squigulator_simulated_data_NoVariants/run1_GRCh38.p14_human_genome |
Squigulator simulation:
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#!/bin/bash -l
#PBS -N squigulator_GRCh38.p14
#PBS -l walltime=48:00:00
#PBS -l mem=64gb
#PBS -l ncpus=32
#use current working directory
cd $PBS_O_WORKDIR
#################################################
## user defined variables
#################################################
SQUIGULATOR='/work/GRC_collaborations/EBV/tools/squigulator-v0.3.0/squigulator'
SAMPLEID='GRCh38.p14'
GENOME='/work/GRC_collaborations/EBV/Genomes/GCF_000001405.40_GRCh38.p14_genomic.fna'
COVERAGE=30
PROFILE='dna-r10-prom'
#################################################
#STEP1: Create simulated reads at 30X genome coverage
#example code:
#squigulator hg38noAlt.fa -x dna-r10-prom -o reads.blow5 -f 30
#we use the user defined variables above to modify the example code:
$SQUIGULATOR $GENOME -x $PROFILE \
-o ${SAMPLEID}_ONT_${PROFILE}_reads.blow5 \
-f $COVERAGE \
-t 32 \
-q ${SAMPLEID}_ONT_${PROFILE}_reads.fasta \
-c ${SAMPLEID}_ONT_${PROFILE}_reads_aln.paf \
-a ${SAMPLEID}_ONT_${PROFILE}_reads_aln.sam |
EBV_ASM240226v1 ONT simulated data:
Location:
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/work/GRC_collaborations/EBV/analysis/1.squigulator_simulated_data_NoVariants/run2_ASM240226v1_viral_genome |
Squigulator simulation:
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#!/bin/bash -l
#PBS -N squigulator_EBV
#PBS -l walltime=24:00:00
#PBS -l mem=32gb
#PBS -l ncpus=16
#use current working directory
cd $PBS_O_WORKDIR
#################################################
## user defined variables
#################################################
SQUIGULATOR='/work/GRC_collaborations/EBV/tools/squigulator-v0.3.0/squigulator'
SAMPLEID='EBV_ASM240226v1'
GENOME='/work/GRC_collaborations/EBV/Genomes/GCF_002402265.1_ASM240226v1_genomic.fna'
COVERAGE=30
PROFILE='dna-r10-prom'
#################################################
#STEP1: Create simulated reads at 30X genome coverage
#example code:
#squigulator hg38noAlt.fa -x dna-r10-prom -o reads.blow5 -f 30
#we use the user defined variables above to modify the example code:
$SQUIGULATOR $GENOME -x $PROFILE \
-o ${SAMPLEID}_ONT_${PROFILE}_reads.blow5 \
-f $COVERAGE \
-t 16 \
-q ${SAMPLEID}_ONT_${PROFILE}_reads.fasta \
-c ${SAMPLEID}_ONT_${PROFILE}_reads_aln.paf \
-a ${SAMPLEID}_ONT_${PROFILE}_reads_aln.sam |
GRCh38.p14+EBV_ASM240226v1 ONT simulated data:
Locations:
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/work/GRC_collaborations/EBV/analysis/1.squigulator_simulated_data_NoVariants/run3_custom_genome_human+virus |
Squigulator simulation:
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#!/bin/bash -l
#PBS -N squigulator_GRCh38.p14_EBV
#PBS -l walltime=48:00:00
#PBS -l mem=64gb
#PBS -l ncpus=32
#use current working directory
cd $PBS_O_WORKDIR
#################################################
## user defined variables
#################################################
SQUIGULATOR='/work/GRC_collaborations/EBV/tools/squigulator-v0.3.0/squigulator'
SAMPLEID='GRCh38.p14_EBV_custom_genome'
GENOME='/work/GRC_collaborations/EBV/Genomes/custom_genome_one_GCF.fna'
COVERAGE=30
PROFILE='dna-r10-prom'
#################################################
#STEP1: Create simulated reads at 30X genome coverage
#example code:
#squigulator hg38noAlt.fa -x dna-r10-prom -o reads.blow5 -f 30
#we use the user defined variables above to modify the example code:
$SQUIGULATOR $GENOME -x $PROFILE \
-o ${SAMPLEID}_ONT_${PROFILE}_reads.blow5 \
-f $COVERAGE \
-t 32 \
-q ${SAMPLEID}_ONT_${PROFILE}_reads.fasta \
-c ${SAMPLEID}_ONT_${PROFILE}_reads_aln.paf \
-a ${SAMPLEID}_ONT_${PROFILE}_reads_aln.sam |
Outputs include:
BLOW5: simulated ONT data using dna-r10-prom profile at 30X genome coverage (*
reads.blow5)FASTA: FASTA file to write simulated reads with no errors (*
reads.fasta)PAF: PAF file to write the alignment of simulated reads (*
reads_aln.paf)SAM: SAM file to write the alignment of simulated reads (*
reads_aln.sam)