Modules related to Nanopore sequencing

Usage

module load bioinfo-ugrp-modules
module load Guppy
# If needed:
module load Rerio

Note that for GPU acceleration on Saion, srun needs -pgpu --gres gpu:1 and guppy_basecaller needs --device auto.

Please ask further questions on the BioinfoUgrp group on Teams (OIST login needed).

Guppy

Homepage: https://community.nanoporetech.com/protocols/Guppy-protocol
Source code: Proprietary.

Example module update on Saion

VER=6.5.7
cd /bucket/BioinfoUgrp/Guppy/
wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-${VER}-1.el7.x86_64.rpm
rpm2cpio ont-guppy-${VER}-1.el7.x86_64.rpm | cpio -idmv
mkdir $VER
mv opt $VER
cd /apps/.bioinfo-ugrp-modulefiles/Guppy
cp 2.3.5 $VER

Example commands for running Guppy on Saion

module load bioinfo-ugrp-modules
module load Guppy
srun --time 2-0 --mem 20G -pgpu --gres gpu:1 --pty guppy_basecaller \
   -i <where FAST5 files are> \
   --recursive \
   --flowcell FLO-MIN106 --kit SQK-LSK109 \
   --num_callers 16 --device auto \
   --records_per_fastq 0 --qscore_filtering --min_qscore 7 --calib_detect \
   -s <where to write the output>

Dorado

Homepage: https://github.com/nanoporetech/dorado
License: Oxford Nanopore Technologies PLC. Public License Version 1.0

Example module update on Saion

VER=0.7.3
cd /bucket/BioinfoUgrp/Nanopore/Dorado/
FILE_TO_DOWNLOAD=dorado-${VER}-linux-x64.tar.gz
wget https://cdn.oxfordnanoportal.com/software/analysis/$FILE_TO_DOWNLOAD 
tar xvfz $FILE_TO_DOWNLOAD
rm $FILE_TO_DOWNLOAD
mv dorado-${VER}* $VER
cd /apps/.bioinfo-ugrp-modulefiles/Dorado
cp 0.7.0 $VER

The config file contains:

#%Module1.0##################################################################
#
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    /bucket/BioinfoUgrp/$appname/$appversion

## URL of application homepage:
set appurl     https://github.com/nanoporetech/dorado

## Short description of package:
module-whatis   "A LibTorch Basecaller for Oxford Nanopore Reads"

## Load any needed modules:
module load Dorado-models

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
prepend-path    PATH            $apphome/bin
prepend-path    LD_LIBRARY_PATH $apphome/lib

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...

Dorado models

The basecall models are distributed separately and can be downloaded with the dorado command. They are also available as a Dorado-models module that exports their path to the $DORADO_MODELS environment variable, and which is loaded by the Dorado module.

At the moment the contents of the Dorado-models/latest module are downloaded by hand in /bucket/BioinfoUgrp/Dorado-models/latest/ with the dorado download command.

The module config file contains:

#%Module1.0##################################################################
#
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    /bucket/BioinfoUgrp/$appname/$appversion

## URL of application homepage:
set appurl     https://github.com/nanoporetech/dorado

## Short description of package:
module-whatis   "Basecalling models and configuration files for Dorado"

## Load any needed modules:

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
setenv DORADO_MODELS $apphome

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...

Example commands for running Dorado on Saion

module load bioinfo-ugrp-modules
module load Dorado
# See the help:
srun -pgpu dorado basecaller -h
# Note that Dorado does not work with the P100 cards.
srun -pgpu --gres gpu:V100:1 --pty --mem 20G dorado basecaller $DORADO_MODELS/the_model_you_want path_to_POD5_or_FAST5_files

Rerio

Homepage: https://github.com/nanoporetech/rerio
Source code: Proprietary (the GitHub repository is only a facility to dowload the models from ONT).

Notes on module creation on Saion

Important: there are some additions and deletions of models without change of version number. In that case I download and add the models by hand, without removing the old ones.

2021/03: addition of v032 CRF models (https://github.com/nanoporetech/rerio/commit/3bc3a94c7a396a85026958e04a0be5a84c352397)

VER=4.4.0
cd /bucket/BioinfoUgrp/Rerio/
git clone https://github.com/nanoporetech/rerio rerio-GitHub-$VER
cd rerio-GitHub-$VER
git checkout $VER
./download_model.py
cp -a basecall_models ../$VER
cp /bucket/BioinfoUgrp/Guppy/4.4.0/ont/guppy/data/lambda_3.6kb.fasta ../$VER

cd /apps/.bioinfo-ugrp-modulefiles/Rerio
cat > $VER<< '__END__'
#%Module1.0##################################################################
#
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    /bucket/BioinfoUgrp/$appname/$appversion

## URL of application homepage:
set appurl     https://github.com/nanoporetech/rerio

## Short description of package:
module-whatis   "research release basecalling models and configuration files"

## Load any needed modules:

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
setenv RERIO_MODELS $apphome

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...
__END__

Example commands for running Guppy on Saion

module load bioinfo-ugrp-modules
module load Guppy
module load Rerio
srun --time 2-0 --mem 20G -pgpu --gres gpu:1 --pty \
  guppy_basecaller \
    -i <fast5dir> \
    --recursive \
    -d $RERIO_MODELS \
    -c res_dna_r941_min_crf_v031.cfg \
    --num_callers 16 \
    --records_per_fastq 0 \
    --qscore_filtering --min_qscore 7 \
    --calib_detect \
    -s <outputdir>\
    --device auto

Medaka

Homepage: https://github.com/nanoporetech/medaka
Source code: MPL-2.0 License

VER=1.3.2
module load python/3.7.3
module load ont-fast5-api
APP=medaka
MODROOT=/bucket/BioinfoUgrp/
APPDIR=$MODROOT/$APP
mkdir -p $APPDIR/$VER
cd $APPDIR/$VER
PYTHONUSERBASE=$(pwd) pip3 install --user $APP --no-warn-script-location
cd /apps/.bioinfo-ugrp-modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER
#%Module1.0##################################################################
#
set modulehome /bucket/BioinfoUgrp
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    $modulehome/$appname/$appversion

## URL of application homepage:
set appurl     https://pypi.org/project/medaka/

## Short description of package:
module-whatis   "Tool to create consensus sequences and variant calls from nanopore sequencing data."

## Load any needed modules:
module load python/3.7.3

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
prepend-path    PATH            $apphome/bin
prepend-path    PYTHONPATH      $apphome/lib/python3.7/site-packages/

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...
__END__

ont-fast5-api

Homepage: https://pypi.org/project/ont-fast5-api/
Sourcecode: https://github.com/nanoporetech/ont_fast5_api

Installation on Deigo

module load python/3.7.3
APP=ont_fast5_api
MODROOT=/bucket/BioinfoUgrp/
APPDIR=$MODROOT/$APP
VER=3.3.0
mkdir -p $APPDIR/$VER
cd $APPDIR/$VER
PYTHONUSERBASE=$(pwd) pip3 install --user ont_fast5_api
cd /apps/.bioinfo-ugrp-modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER.lua
-- Default settings
local modroot    = "/bucket/LuscombeU/"
local appname    = myModuleName()
local appversion = myModuleVersion()
local apphome    = pathJoin(modroot, myModuleFullName())

-- Package information
whatis("Name: "..appname)
whatis("Version: "..appversion)
whatis("URL: ".."https://github.com/nanoporetech/ont_fast5_api")
whatis("Category: ".."bioinformatics")
whatis("Keywords: ".."Nanopore, sequence")
whatis("Description: ".." Oxford Nanopore Technologies fast5 API software.")

help([[ont_fast5_api installed with pip

See https://github.com/nanoporetech/ont_fast5_api for help.]])

-- Package settings
depends_on("python/3.7.3")
prepend_path("PATH", apphome.."/bin")
prepend_path("PYTHONPATH", apphome.."/lib/python3.7/site-packages")
__END__

Installation on Saion

module load python/3.7.3
APP=ont_fast5_api
MODROOT=/bucket/BioinfoUgrp/
APPDIR=$MODROOT/$APP
VER=3.3.0
mkdir -p $APPDIR/$VER
cd $APPDIR/$VER
PYTHONUSERBASE=$(pwd) pip3 install --user ont_fast5_api
cd /apps/.bioinfo-ugrp-modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER
#%Module1.0##################################################################
#
set modulehome /bucket/BioinfoUgrp
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    $modulehome/$appname/$appversion

## URL of application homepage:
set appurl     https://pypi.org/project/ont-fast5-api/

## Short description of package:
module-whatis   "Oxford Nanopore Technologies fast5 API software"

## Load any needed modules:
module load python/3.7.3

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
prepend-path    PATH            $apphome/bin
prepend-path    PYTHONPATH      $apphome/lib/python3.7/site-packages/

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...
__END__

POD5 Python Package

Appears to be the successor of pod5-format-tools

Homepage: https://pypi.org/project/pod5/
Sourcecode: https://github.com/nanoporetech/pod5-file-format

Installation on Saion

module load python/3.7.3
APP=pod5
MODROOT=/bucket/BioinfoUgrp/
APPDIR=$MODROOT/$APP
VER=0.1.5
mkdir -p $APPDIR/$VER
cd $APPDIR/$VER
PYTHONUSERBASE=$(pwd) pip3 install --user --upgrade pip
PYTHONUSERBASE=$(pwd) bin/pip3 install --user --upgrade $APP
cd /apps/.bioinfo-ugrp-modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER
#%Module1.0##################################################################
#
set modulehome /bucket/BioinfoUgrp
set appname    [lrange [split [module-info name] {/}] 0 0]
set appversion [lrange [split [module-info name] {/}] 1 1]
set apphome    $modulehome/$appname/$appversion

## URL of application homepage:
set appurl     https://pypi.org/project/pod5-format-tools/

## Short description of package:
module-whatis   "Oxford Nanopore Technologies POD5 tools"

## Load any needed modules:
module load python/3.7.3

## Modify as needed, removing any variables not needed.  Non-path variables
## can be set with "setenv VARIABLE value".
prepend-path    PATH            $apphome/bin
prepend-path    PYTHONPATH      $apphome/lib/python3.7/site-packages/

## These lines are for logging module usage.  Don't remove them:
set modulefile [lrange [split [module-info name] {/}] 0 0]
set version    [lrange [split [module-info name] {/}] 1 1]
set action     [module-info mode]
system logger -t module -p local6.info DATE=\$(date +%FT%T),USER=\$USER,JOB=\$\{SLURM_JOB_ID=NOJOB\},APP=$modulefile,VERSION=$version,ACTION=$action
## Don't remove this line!  For some reason, it has to be here...
__END__

vbz compression plugin

Homepage: https://github.com/nanoporetech/vbz_compression
Sourcecode: https://github.com/nanoporetech/vbz_compression

Installation on Deigo

APP=vbz_compression
MODROOT=/bucket/BioinfoUgrp/Other
APPDIR=$MODROOT/$APP
VER=1.0.2
mkdir -p $APPDIR/$VER
cd $APPDIR/$VER
wget https://github.com/nanoporetech/vbz_compression/releases/download/1.0.2/ont-vbz-hdf-plugin_${VER}-1.focal_amd64.deb
mkdir hdf_plugin
dpkg --fsys-tarfile ont-vbz-hdf-plugin_${VER}-1.focal_amd64.deb | tar xOf - ./usr/local/hdf5/lib/plugin/libvbz_hdf_plugin.so > hdf_plugin/libvbz_hdf_plugin.so
cd $MODROOT/modulefiles/
mkdir -p $APP
cat <<'__END__' > $APP/$VER.lua
-- Default settings
local modroot    = "/bucket/BioinfoUgrp"
local appname    = myModuleName()
local appversion = myModuleVersion()
local apphome    = pathJoin(modroot, myModuleFullName())

-- Package information
whatis("Name: "..appname)
whatis("Version: "..appversion)
whatis("URL: ".."https://github.com/nanoporetech/vbz_compression")
whatis("Category: ".."bioinformatics")
whatis("Keywords: ".."Nanopore, sequence")
whatis("Description: ".." Oxford Nanopore Technologies vbz HDF5 plugin.")

help([[ont_fast5_api installed with pip

See [https://github.com/nanoporetech/ont_fast5_api](https://github.com/nanoporetech/vbz_compression) for help.]])

-- Package settings
setenv("HDF5_PLUGIN_PATH", apphome.."/hdf_plugin")
__END__

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NanoporeModules.md

NanoporeModules.md

Modules related to Nanopore sequencing

Usage

Guppy

Example module update on Saion

Example commands for running Guppy on Saion

Dorado

Example module update on Saion

Dorado models

Example commands for running Dorado on Saion

Rerio

Notes on module creation on Saion

Example commands for running Guppy on Saion

Medaka

ont-fast5-api

Installation on Deigo

Installation on Saion

POD5 Python Package

Installation on Saion

vbz compression plugin

Installation on Deigo

Files

NanoporeModules.md

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History

NanoporeModules.md

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Modules related to Nanopore sequencing

Usage

Guppy

Example module update on Saion

Example commands for running Guppy on Saion

Dorado

Example module update on Saion

Dorado models

Example commands for running Dorado on Saion

Rerio

Notes on module creation on Saion

Example commands for running Guppy on Saion

Medaka

ont-fast5-api

Installation on Deigo

Installation on Saion

POD5 Python Package

Installation on Saion

vbz compression plugin

Installation on Deigo