Table of Contents
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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.
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cp slow5tools $HOME/bin/ |
Example data:
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/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:
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./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. |