Table of Contents
...
| Code Block |
|---|
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.
...
| Code Block |
|---|
cp slow5tools $HOME/bin/ |
Example data:
| Code Block |
|---|
/work/GRC_collaborations/EBV/analysis/1.squigulator_simulated_data_NoVariants/coverage_5x/run2_ASM240226v1_viral_genome/EBV_ASM240226v1_ONT_dna-r10-prom_reads_5x.blow5 |
slow5tools parameters:
| Code Block |
|---|
./slow5tools --help Usage: ./slow5tools [OPTIONS] [COMMAND] [ARG] Tools for using slow5 files. OPTIONS: -h, --help Display this message and exit. -v, --verbose Verbosity level. -V, --version Output version information and exit. --cite Prints the citation. COMMANDS: f2s or fast5toslow5 convert fast5 file(s) to SLOW5/BLOW5 s2f or slow5tofast5 convert SLOW5/BLOW5 file(s) to fast5 merge merge SLOW5/BLOW5 files split split SLOW5/BLOW5 files index create a SLOW5/BLOW5 index file get display the read entry for each specified read id view view the contents of a SLOW5/BLOW5 file or convert between different SLOW5/BLOW5 formats and compressions stats prints statistics of a SLOW5/BLOW5 file to the stdout cat quickly concatenate SLOW5/BLOW5 files of same type (same header, extension, compression)] quickcheck quickly checks if a SLOW5/BLOW5 file is intact skim skims through requested components in a SLOW5/BLOW5 file ARGS: Try './slow5tools [COMMAND] --help' for more information. |
Convert slow5 to fast5 - options:
| Code Block |
|---|
Convert SLOW5/BLOW5 files to FAST5 format.
Usage: ./slow5tools s2f [OPTIONS] -d [OUT_DIR] [SLOW5_FILE/DIR] ...
OPTIONS:
-d, --out-dir DIR output to directory
-o, --output FILE output to FILE [stdout]
-p, --iop INT number of I/O processes [8]
-h, --help display this message and exit |
Running slow5rools:
| Code Block |
|---|
#PBS -N Convert_EBV
#PBS -l walltime=24:00:00
#PBS -l mem=16gb
#PBS -l ncpus=8
#PBS -m abe
#PBS -o convert_blow5_to_fast5_output.log
#PBS -e convert_blow5_to_fast5_error.log
#Positive control
###Simulated data: convert BLOW5 to FAST5 for wf-basecalling
#### Note: Adjust the path directories
# Change to the directory where the job was submitted
cd $PBS_O_WORKDIR
# Load the necessary modules
module load slow5tools
# Define path directories as a variable
BLOW5_FILE='GRCh38.p14_ONT_dna-r10-prom_reads_5x.blow5'
FAST5_FILE='GRCh38.p14_ONT_dna-r10-prom_reads_5x.fast5'
SLOW5TOOLS='/work/GRC_collaborations/EBV/tools/slow5tools-v1.1.0/slow5tools'
# Ensure the output directory exists
# when multiple slow5 files are available then use -d outpur_dir option rather than -o converted.fastq file (see below)
#mkdir -p ${OUT_DIR}
# Run the conversion
#slow5tools tofast5 -o ${FAST5_FILE} ${BLOW5_FILE}
$SLOW5TOOLS s2f -p 8 -o ${FAST5_FILE} ${BLOW5_FILE} |