Software and dataset
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who?latest PL-Gridsoftwarelinkversioncommentsinstall command for apt, pip, conda, biocbase commandver on Prometheusin moduleVM 14VM 15
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sudo apt install
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condahttps://conda.io/miniconda.htmlconda install 4.5.10plgrid/tools/python-intel/3.6.2
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Basecalling
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human SVnanonethttps://bioconda.github.io/recipes/nanonet/README.htmlconda install nanonetYes
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human SVnanocallhttps://github.com/mateidavid/nanocallconda install nanocallYes
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human SVdeepnanohttps://bitbucket.org/vboza/deepnano/downloads/sudo apt install deepnanoYes
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human SValbacorehttps://github.com/NGSchoolEU/2018#pip3see READMEYesYes
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QC:
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human SVnanoFilt
https://poretools.readthedocs.io/en/latest/content/installation.html#basic-installation
python 2.7!sudo apt install nanofiltYes
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human SVnanoFilthttps://github.com/wdecoster/nanofiltpip3 install nanofiltYes
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AndreyPFastQChttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/not mandatoryYesYes
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Assembly:
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human SV1.9.7Canuhttps://github.com/marbl/canuconda install canuYes
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human SV
3.8.0 - update needed!!
SPAdeshttp://cab.spbu.ru/software/spades/3.12.0conda install spadesYes
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miniasmhttps://github.com/lh3/miniasmconda install miniasmYes
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RobertVralahttps://github.com/rvaser/ralaconda install ralaYes
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RobertVraconhttps://github.com/isovic/raconconda install raconYes
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Alignment:
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human SVBlasRconda install -c bioconda blasrconda install blasrYes
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human SVlast-alignhttp://last.cbrc.jp/doc/last.htmlv953sudo apt install last-alignYes
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human SVminimap2https://github.com/lh3/minimap2conda install minimap2Yes
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human SVngmlrhttps://github.com/philres/ngmlrconda install ngmlrYes
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human SV0.7.12BWAhttps://github.com/lh3/bwaconda install bwaYes
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RobertVedlibhttps://github.com/martinsos/edlibconda install edlibYes
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SNV:
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human SVnanopolishhttps://github.com/jts/nanopolishconda install nanopolishYes
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SV:
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human SVSniffelshttps://github.com/fritzsedlazeck/SnifflesYes
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human SVPBSuitehttps://sourceforge.net/projects/pb-jelly/PBHoneyYes
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human SVPickyhttps://github.com/TheJacksonLaboratory/Picky/releasesv0.2.aYes
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Variant Annotation:
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human SVAnnotSVhttp://lbgi.fr/AnnotSV/downloadsYes
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human SV4.3tSNPeffhttp://snpeff.sourceforge.net/download.htmlconda install snpeffYes
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human SV92.4VEPhttps://github.com/Ensembl/ensembl-vepYes
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Nanopore alignment etc
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AndreyPseqtkhttps://github.com/lh3/seqtkconda install seqtkYes
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AndreyPsamtoolshttp://samtools.sourceforge.net/conda install samtoolsYes
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AndreyPigvhttp://software.broadinstitute.org/software/igv/
sudo apt version fails!!
conda install igvYes
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AndreyP1.9.7Canuhttps://github.com/marbl/canuconda install canuYes
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AndreyPSPAdeshttp://cab.spbu.ru/software/spades/3.12.0conda install spadesYes
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AndreyPFastQChttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/Yes
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AndreyPminimap2https://github.com/lh3/minimap2conda install minimap2Yes
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AndreyPQuasthttps://github.com/ablab/quastconda install quastYes
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AndreyP0.7.12BWAhttps://github.com/lh3/bwaconda install bwaYes
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RobertVBandagehttps://rrwick.github.io/Bandage/conda install bandageYes
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RobertVQuasthttps://github.com/ablab/quastconda install quastYes
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RobertVBUSCOhttps://gitlab.com/ezlab/buscoconda install buscoYes
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RobertVGepardhttp://cube.univie.ac.at/gepardYes
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human SV2.27.1bedtools
https://bedtools.readthedocs.io/en/latest/content/installation.html
conda install bedtoolsYes
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human SVg++8.1.0plgrid/tools/gcc/8.1.0YesYes
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human SV1.8.10hdf5>=1.8.71.10.1plgrid/libs/hdf5/1.10.1YesYes
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human SV1.2.11zlibYesYes
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human SV1.9Java >=v1.7YesYes
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human SV8.6.4TCLhttp://tcl.tk/software/tcltk/
human SV
sudo apt install TCL8.6.4plgrid/tools/tcltk/8.6.4-threadsYes
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human SV2.7.3Pythonv2.7
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human SVpython-pip
do python v2.6
sudo apt install python-pipsudo pip install -U YesYes
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human SV1.66biopython
do python v2.7
Python package
sudo pip install -U biopython
YesYes
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human SV1.1.0matplotlib
do python v2.7
Python package
sudo pip install -U matplotlib
YesYes
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human SVseaborn
do python v2.7
Python package
sudo pip install -U seabornYesYes
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human SVpandas
do python v2.7
Python package
sudo pip install -U pandasYesYes
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human SVcython0.23.4
Python package
sudo pip install -U cythonYesYes
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human SV1.7.1numpy1.10.2
Python package
sudo pip install -U numpyYesYes
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human SVh5py2.5.0
Python package
sudo pip install -U h5pyYesYes
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human SVTheanohttps://github.com/Theano/Theano0.7.0
Python package
sudo pip install -U TheanoYesYes
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human SVpython-dateutil2.5.0
Python package
sudo pip install -U python-dateutil
YesYes
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all3.4Pythonv2.7sudo apt install python-pip3sudo pip3 install -U 3.6.2plgrid/tools/python-intel/3.6.2
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allalbacorev3.2.2
Python package
sudo pip3 install path/to/ont_albacore-xxx_x86_64.whl
YesYes
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mtDNAnanoplothttps://github.com/wdecoster/NanoPlotpip3 install nanoplotYes
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mtDNAporechophttps://github.com/rrwick/Porechop
git clone https://github.com/rrwick/Porechop.git; cd Porechop; sudo python3 setup.py install; porechop -h
Yes
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mtDNAnanopolishhttps://github.com/jts/nanopolish
git clone --recursive https://github.com/jts/nanopolish.git; cd nanopolish; make
Yes
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Tabletconda install tabletYes
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Rv3.4install.packages('3.4.4plgrid/apps/r/3.4.4YesYes
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mtDNAtidyverseinstall.packages('tidyverse')Yes
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mtDNAdata.table
install.packages('data.table')
Yes
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devtoolsinstall.packages('devtools')
devtools::install_github('
YesYes
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mtDNA
gabraham/flashpca/flashpcaR
https://github.com/gabraham/flashpca/
devtools::install_github('gabraham/flashpca/flashpcaR')
Yes
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biochttps://bioconductor.org/install/
source("https://bioconductor.org/biocLite.R"); biocLite()
source('https://bioconductor.org/biocLite.R'); biocLite('
YesYes
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human SV
GenomicRanges
source('https://bioconductor.org/biocLite.R'); biocLite('GenomicRanges')
YesYes
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microbiomPython2.7.9YesYes
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