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.gitmodules
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[submodule "ancestree"]
path = ancestree
url = https://github.com/MathildeFogPerez/ancestree
[submodule "AnnapuRNA"]
path = AnnapuRNA
url = https://github.com/filipspl/AnnapuRNA
[submodule "PatchInference"]
path = PatchInference
url = https://github.com/hzi-bifo/PatchInference
[submodule "fieldbioinformatics"]
path = fieldbioinformatics
url = https://github.com/artic-network/fieldbioinformatics
[submodule "augur"]
path = augur
url = https://github.com/nextstrain/augur
[submodule "bertax"]
path = bertax
url = https://github.com/f-kretschmer/bertax
[submodule "CAMISIM"]
path = CAMISIM
url = https://github.com/CAMI-challenge/CAMISIM
[submodule "CCHFV-PrimerChecker"]
path = CCHFV-PrimerChecker
url = https://github.com/cesaregruber/CCHFV-PrimerChecker
[submodule "Cenote-Taker2"]
path = Cenote-Taker2
url = https://github.com/mtisza1/Cenote-Taker2
[submodule "CIAlign"]
path = CIAlign
url = https://github.com/KatyBrown/CIAlign
[submodule "ena-upload-cli"]
path = ena-upload-cli
url = https://github.com/usegalaxy-eu/ena-upload-cli
[submodule "cojac"]
path = cojac
url = https://github.com/cbg-ethz/cojac
[submodule "CovidStrategyCalculator"]
path = CovidStrategyCalculator
url = https://github.com/CovidStrategyCalculator/CovidStrategyCalculator
[submodule "covigator-ngs-pipeline"]
path = covigator-ngs-pipeline
url = https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline
[submodule "dark-matter"]
path = dark-matter
url = https://github.com/acorg/dark-matter
[submodule "darkq"]
path = darkq
url = https://github.com/phiweger/darkq
[submodule "DeepVirFinder"]
path = DeepVirFinder
url = https://github.com/jessieren/DeepVirFinder
[submodule "dinuq"]
path = dinuq
url = https://github.com/spyros-lytras/dinuq
[submodule "DRUMMER"]
path = DRUMMER
url = https://github.com/DepledgeLab/DRUMMER
[submodule "DVGfinder"]
path = DVGfinder
url = https://github.com/MJmaolu/DVGfinder
[submodule "efinder"]
path = efinder
url = https://github.com/gruberlab/efinder
[submodule "epa-ng"]
path = epa-ng
url = https://github.com/Pbdas/epa-ng
[submodule "EpiDope"]
path = EpiDope
url = https://github.com/mcollatz/EpiDope
[submodule "epitope-prediction"]
path = epitope-prediction
url = https://github.com/hzi-bifo/epitope-prediction
[submodule "ESCA"]
path = ESCA
url = https://github.com/cesaregruber/ESCA
[submodule "EvaTargetedCovid19Testing"]
path = EvaTargetedCovid19Testing
url = https://github.com/vgupta1/EvaTargetedCovid19Testing
[submodule "GInPipe"]
path = GInPipe
url = https://github.com/KleistLab/GInPipe
[submodule "Haploflow"]
path = Haploflow
url = https://github.com/hzi-bifo/Haploflow
[submodule "hecatomb"]
path = hecatomb
url = https://github.com/shandley/hecatomb
[submodule "HIV-phyloTSI"]
path = HIV-phyloTSI
url = https://github.com/BDI-pathogens/HIV-phyloTSI
[submodule "hmmprospector"]
path = hmmprospector
url = https://github.com/gruberlab/hmmprospector
[submodule "HoloVir"]
path = HoloVir
url = https://github.com/plaffy/HoloVir
[submodule "iva"]
path = iva
url = https://github.com/sanger-pathogens/iva
[submodule "Jovian"]
path = Jovian
url = https://github.com/DennisSchmitz/Jovian
[submodule "MARVEL"]
path = MARVEL
url = https://github.com/LaboratorioBioinformatica/MARVEL
[submodule "MC-CBN"]
path = MC-CBN
url = https://github.com/cbg-ethz/MC-CBN
[submodule "Meta-CATS"]
path = Meta-CATS
url = https://github.com/JCVenterInstitute/Meta-CATS
[submodule "MetaPhage"]
path = MetaPhage
url = https://github.com/MattiaPandolfoVR/MetaPhage
[submodule "MetaPhinder"]
path = MetaPhinder
url = https://github.com/vanessajurtz/MetaPhinder
[submodule "metapop"]
path = metapop
url = https://github.com/metaGmetapop/metapop
[submodule "MUFFIN"]
path = MUFFIN
url = https://github.com/RVanDamme/MUFFIN
[submodule "multiPhATE"]
path = multiPhATE
url = https://github.com/carolzhou/multiPhATE
[submodule "mVIRs"]
path = mVIRs
url = https://github.com/SushiLab/mVIRs
[submodule "OGRE"]
path = OGRE
url = https://github.com/Marleen1/OGRE
[submodule "Pathway2Targets"]
path = Pathway2Targets
url = https://github.com/bpickett/Pathway2Targets
[submodule "PhageBoost"]
path = PhageBoost
url = https://github.com/ku-cbd/PhageBoost
[submodule "PhaMers"]
path = PhaMers
url = https://github.com/jondeaton/PhaMers
[submodule "PHANOTATE"]
path = PHANOTATE
url = https://github.com/deprekate/PHANOTATE
[submodule "phigaro"]
path = phigaro
url = https://github.com/bobeobibo/phigaro
[submodule "PhiSpy"]
path = PhiSpy
url = https://github.com/linsalrob/PhiSpy
[submodule "PHIST"]
path = PHIST
url = https://github.com/refresh-bio/PHIST
[submodule "poreCov"]
path = poreCov
url = https://github.com/replikation/poreCov
[submodule "poseidon"]
path = poseidon
url = https://github.com/hoelzer/poseidon
[submodule "PoW_model"]
path = PoW_model
url = https://github.com/mg878/PoW_model
[submodule "PPR-Meta"]
path = PPR-Meta
url = https://github.com/zhenchengfang/PPR-Meta
[submodule "PrEP"]
path = PrEP
url = https://github.com/KleistLab/PrEP
[submodule "PriSeT"]
path = PriSeT
url = https://github.com/mariehoffmann/PriSeT
[submodule "ProphET"]
path = ProphET
url = https://github.com/jaumlrc/ProphET
[submodule "pvogs_function"]
path = pvogs_function
url = https://github.com/MGXlab/pvogs_function
[submodule "Quasimodo"]
path = Quasimodo
url = https://github.com/hzi-bifo/Quasimodo
[submodule "RESEQ"]
path = RESEQ
url = https://github.com/babaksaremi/RESEQ
[submodule "santa-sim"]
path = santa-sim
url = https://github.com/santa-dev/santa-sim
[submodule "sars2seq"]
path = sars2seq
url = https://github.com/virologyCharite/sars2seq
[submodule "seeker"]
path = seeker
url = https://github.com/gussow/seeker
[submodule "silentMutations"]
path = silentMutations
url = https://github.com/desiro/silentMutations
[submodule "spacepharer"]
path = spacepharer
url = https://github.com/soedinglab/spacepharer
[submodule "SDplots"]
path = SDplots
url = https://github.com/hzi-bifo/SDplots
[submodule "tabajara"]
path = tabajara
url = https://github.com/gruberlab/tabajara
[submodule "TreeKnit.jl"]
path = TreeKnit.jl
url = https://github.com/PierreBarrat/TreeKnit.jl
[submodule "vadr"]
path = vadr
url = https://github.com/nawrockie/vadr
[submodule "VFM"]
path = VFM
url = https://github.com/liuql2019/VFM
[submodule "VIBRANT"]
path = VIBRANT
url = https://github.com/AnantharamanLab/VIBRANT
[submodule "VIcaller"]
path = VIcaller
url = https://github.com/xunchen85/VIcaller
[submodule "vidhop"]
path = vidhop
url = https://github.com/flomock/vidhop
[submodule "viga"]
path = viga
url = https://github.com/EGTortuero/viga
[submodule "VIGOR4"]
path = VIGOR4
url = https://github.com/JCVenterInstitute/VIGOR4
[submodule "VIP"]
path = VIP
url = https://github.com/keylabivdc/VIP/
[submodule "Viral_Variant_Visualiser"]
path = Viral_Variant_Visualiser
url = https://github.com/ALFLAG/Viral_Variant_Visualiser
[submodule "viralComplete"]
path = viralComplete
url = https://github.com/ablab/viralComplete/
[submodule "ViralFlow"]
path = ViralFlow
url = https://github.com/dezordi/ViralFlow
[submodule "viralMetagenomicsPipeline"]
path = viralMetagenomicsPipeline
url = https://github.com/wclose/viralMetagenomicsPipeline
[submodule "viralrecon"]
path = viralrecon
url = https://github.com/nf-core/viralrecon
[submodule "viralVerify"]
path = viralVerify
url = https://github.com/ablab/viralVerify/
[submodule "ViraMiner"]
path = ViraMiner
url = https://github.com/NeuroCSUT/ViraMiner
[submodule "virAnnot"]
path = virAnnot
url = https://github.com/marieBvr/virAnnot
[submodule "VirFinder"]
path = VirFinder
url = https://github.com/jessieren/VirFinder
[submodule "emg-viral-pipeline"]
path = emg-viral-pipeline
url = https://github.com/EBI-Metagenomics/emg-viral-pipeline
[submodule "virMine"]
path = virMine
url = https://github.com/thatzopoulos/virMine
[submodule "VirMiner"]
path = VirMiner
url = https://github.com/TingtZHENG/VirMiner
[submodule "virnet"]
path = virnet
url = https://github.com/alyosama/virnet
[submodule "VirSorter"]
path = VirSorter
url = https://github.com/simroux/VirSorter
[submodule "virulign"]
path = virulign
url = https://github.com/rega-cev/virulign
[submodule "virus_prediction"]
path = virus_prediction
url = https://github.com/rujinlong/virus_prediction
[submodule "ViruSpy"]
path = ViruSpy
url = https://github.com/NCBI-Hackathons/ViruSpy
[submodule "What_the_Phage"]
path = What_the_Phage
url = https://github.com/replikation/What_the_Phage
[submodule "ncov_minipipe"]
path = ncov_minipipe
url = https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe
[submodule "deepac"]
path = deepac
url = https://gitlab.com/dacs-hpi/deepac
[submodule "deepac-live"]
path = deepac-live
url = https://gitlab.com/dacs-hpi/deepac-live
[submodule "ganon"]
path = ganon
url = https://github.com/pirovc/ganon.git
[submodule "LiveKraken"]
path = LiveKraken
url = https://gitlab.com/rki_bioinformatics/LiveKraken
[submodule "purple"]
path = purple
url = https://gitlab.com/rki_bioinformatics/purple
[submodule "TaxIt"]
path = TaxIt
url = https://gitlab.com/mkuhring/TaxIt
[submodule "SpikeProSARS-CoV-2"]
path = SpikeProSARS-CoV-2
url = https://github.com/3BioCompBio/SpikeProSARS-CoV-2
[submodule "DeePaC"]
path = DeePaC
url = https://github.com/JakubBartoszewicz/DeePaC.git
[submodule "bioconda-recipes"]
path = bioconda-recipes
url = https://github.com/bioconda/bioconda-recipes.git
[submodule "DeePaC-vir"]
path = DeePaC-vir
url = https://github.com/JakubBartoszewicz/DeePaC-vir.git