BioHPC Cloud Software
There are 1244 software titles installed in BioHPC Cloud. The sofware is available on all machines (unless stated otherwise in notes), complete list of programs is below, please click on a title to see details and instructions. Tabular list of software is available here
Please read details and instructions before running any program, it may contain important information on how to properly use the software in BioHPC Cloud.
3D Slicer, 3d-dna, 454 gsAssembler or gsMapper, 7zip, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, AF_unmasked, AFProfile, AGAT, agrep, albacore, Alder, AliTV-Perl interface, AlleleSeq, ALLMAPS, ALLPATHS-LG, Alphafold, Alphafold3, alphapickle, Alphapulldown, AlphScore, Amber, AMOS, AMPHORA, amplicon.py, AMRFinder, analysis, ANGSD, AnnotaPipeline, Annovar, ant, antiSMASH, anvio, apollo, arcs, ARGweaver, aria2, ariba, Arlequin, ART, ASEQ, aspera, assembly-stats, aster, ASTRAL, atac-seq-pipeline, ataqv, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, atom, ATSAS, Augustus, autocycler, AWS command line interface, AWS v2 Command Line Interface, axe, axel, BA3, BactSNP, bakta, BAMdash, bamm, bamsnap, bamsurgeon, bamtools, bamUtil, barcode_splitter, BarNone, Basset, BayeScan, Bayescenv, bayesR, baypass, bazel, BBMap/BBTools, BCFtools, BCL convert, bcl2fastq, BCP, bdbag, Beagle, beagle-lib, BEAST, BEAST X, Beast2, bed2diffs, bedops, BEDtools, bettercallsal, bfc, bgc, bgen, bicycle, BiG-SCAPE, bigQF, bigtools, bigWig, bioawk, biobakery, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, biscuit, Bismark, Blackbird, blasr, BLAST, BLAST_to_BED, blast2go, BLAT, BlobToolKit, BLUPF90, BMGE, bmtagger, bonito, Boost, Bowtie, Bowtie2, BPGA, Bracken, BRAKER, BRAT-NextGen, BRBseqTools, BreedingSchemeLanguage, breseq, brocc, BSBolt, bsmap, BSseeker2, btyper3, BUSCO, BUSCO Phylogenomics, BWA, bwa-mem2, bwa-meth, bwtool, cactus, CAFE, CAFE5, caffe, cagee, canu, Canvas, CAP3, caper, CarveMe, catch, cBar, CBSU RNAseq, CCMetagen, CCTpack, cd-hit, cdbfasta, cdo, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, centrifuge, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, CheckM2, chimera, ChimeraTE, chimerax, chip-seq-pipeline, ChromHMM, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, ClermonTyping, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, CNVnator, coidb, coinfinder, colabfold, CombFold, Comparative-Annotation-Toolkit, compat, CONCOCT, Conda, Conform-gt, Cooler, copyNumberDiff, cortex_var, CoverM, crabs, CRISPRCasFinder, CRISPResso, crispron, Cromwell, CrossMap, CRT, cuda, Cufflinks, curatedMetagenomicDataTerminal, cutadapt, cuteSV, Cytoscape, dadi, dadi-1.6.3_modif, dadi-cli, danpos, DAS_Tool, dashing, DBSCAN-SWA, dDocent, DeconSeq, Deepbinner, deeplasmid, DeepTE, deepTools, Deepvariant, defusion, degenotate, delly, DESMAN, destruct, DETONATE, dfast, diamond, dipcall, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, dmtcp, dnmtools, Docker, dorado, DRAM, dREG, dREG.HD, drep, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, DWGSIM, dynare, ea-utils, earlgrey, ecCodes, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, eggnog-mapper, EIGENSOFT, elai, ElMaven, emacs, EMBLmyGFF3, EMBOSS, EMIRGE, Empress, enfuse, EnTAP, entropy, epa-ng, ephem, epic2, ermineJ, ete3, EukDetect, EukRep, EVE, EVM, exabayes, exonerate, ExpansionHunterDenovo-v0.8.0, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastAAI, FastANI, fastcluster, fastGEAR, FastME, FastML, fastp, FastQ Screen, fastq-multx-1.4.3, fastq_demux, fastq_pair, fastq_species_detector, FastQC, fastqsplitter, fastsimcoal2, fastspar, fastStructure, FastTree, FASTX, fcs, feems, feh, FFmpeg, fgbio, ficle, figaro, Fiji, Filtlong, fineRADstructure, fineSTRUCTURE, FIt-SNE, FlaGs2, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, FRANz, freebayes, FSA, funannotate, FunGene Pipeline, FunOMIC, G-PhoCS, GADMA, GAEMR, Galaxy, Galaxy in Docker, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, GeMoMa, GENECONV, geneid, GeneMark, GeneRax, Genespace, genomad, Genome STRiP, Genome Workbench, GenomeMapper, Genomescope, GenomeThreader, genometools, GenomicConsensus, genozip, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GetOrganelle, gfaviz, GffCompare, gffread, giggle, git, glactools, GlimmerHMM, GLIMPSE, GLnexus, Globus connect personal, GMAP/GSNAP, gmx_MMPBSA, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GONE, GoShifter, gradle, graftM, grammy, GraPhlAn, graphtyper, graphviz, greenhill, GRiD, gridss, Grinder, grocsvs, GROMACS, GroopM, GSEA, gsort, GTDB-Tk, GTFtools, Gubbins, gunc, GUPPY, gvcftools, hail, hal, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, haplostrips, HaploSync, happ, HapSeq2, harpy, HarvestTools, haslr, hdf5, helixer, hget, hh-suite, HiC-Pro, hic_qc, HiCExplorer, HiFiAdapterFilt, hifiasm, hificnv, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, https://github.com/ksahlin/strobealign, hugin, humann, HUMAnN2, hybpiper, hyde, HyLiTE, Hyper-Gen, hyperopt, HyPhy, hyphy-analyses, iAssembler, IBDLD, IBDNe, IBDseq, idba, IDBA-UD, idemux, IDP-denovo, idr, idseq, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, impute5, IMSA-A, INDELseek, infernal, Infomap, inspector, inStrain, inStrain_lite, InStruct, Intel MKL, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, isoseq, itsx, ivar, JaBbA, jags, Jane, java, jbrowse, JCVI, jellyfish, jsalignon/cactus, juicer, julia, jupyter, jupyterlab, kaiju, kallisto, Kent Utilities, keras, khmer, kinfin, king, kma, KMC, KmerFinder, KmerGenie, kneaddata, kraken, KrakenTools, KronaTools, kSNP, kWIP, LACHESIS, lammps, LAPACK, lapels, LAST, lastz, lcMLkin, LDAK, LDBlockShow, LDhat, LeafCutter, leeHom, lep-anchor, Lep-MAP3, LEVIATHAN, lftp, Liftoff, lifton, Lighter, LinkedSV, LINKS, localcolabfold, LocARNA, LocusZoom, lofreq, longranger, Loupe, LS-GKM, LTR_retriever, LUCY, LUCY2, LUMPY, lyve-SET, m6anet, Macaulay2, MACE, MACS, MaCS simulator, MACS2, macs3, maffilter, MAFFT, mafTools, MAGeCK, MAGeCK-VISPR, Magic-BLAST, magick, MAGScoT, MAKER, manta, mapDamage, mapquik, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, mcl, MCscan, MCScanX, mdust, medaka, medusa, medusa2, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, merqury, MetaBAT, MetaBinner, MetaboAnalystR, MetaCache, MetaCRAST, metaCRISPR, metamaps, MetAMOS, MetaPathways, MetaPhlAn, metapop, metaron, MetaVelvet, MetaVelvet-SL, metaWRAP, methpipe, mfeprimer, MGmapper, MicrobeAnnotator, microtrait, MIDAS, MiFish, Migrate-n, mikado, MinCED, minigraph, Minimac3, Minimac4, minimap2, miniprot, mira, miRDeep2, mirge3, miRquant, MISO, MITE-Hunter, MITE-Tracker, MITObim, MitoFinder, mitohelper, MitoHiFi, mity, MiXCR, MixMapper, MKTest, mlift, mlst, MMAP, MMSEQ, MMseqs2, MMTK, MobileElementFinder, modeltest, MODIStsp-2.0.5, module, moments, momi, MoMI-G, mongo, mono, monocle3, mosdepth, mothur, MrBayes, mrcanavar, mrsFAST, msdial, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMandCo, MUMmer, mummer2circos, muscle, MUSIC, Mutation-Simulator, muTect, myte, MZmine, nag-compiler, namfinder, nanocompore, nanofilt, NanoPlot, Nanopolish, nanovar, ncbi_datasets, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, NextPolish2, nf-core/rnaseq, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NGSNGS, ngsplot, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, NLRtracker, Novoalign, NovoalignCS, nQuire, NRSA, ntSynt, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, odgi, OMA, Oneflux, OpenBLAS, openmpi, openslide, openssl, ORFeus, orthodb-clades, OrthoFinder, orthologr, Orthomcl, pacbio, PacBioTestData, PAGIT, pairtools, pal2nal, paleomix, PAML, panacus, panaroo, pandas, pandaseq, pandoc, pangene, PanPhlAn, Panseq, pantools, Parsnp, PASA, PASTEC, PAUP*, pauvre, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, PBSuite, pbsv, pbtk, PCAngsd, pcre, pcre2, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, pharokka, phasedibd, PHAST, phenopath, Phobius, PHRAPL, phykit, PHYLIP, PhyloCSF, phyloFlash, phylonet, phylophlan*, PhyloPhlAn2, phylophlan3, phyluce, PhyML, phyx, Picard, PICRUSt2, pigz, Pilon, Pindel, piPipes, PIQ, piranha, pixy, PlasFlow, platanus, Platypus, plink, plink2, Plotly, plotsr, plumed, pocp, Point Cloud Library, popbam, PopCOGenT, PopLDdecay, Porechop, poretools, portcullis, POUTINE, pplacer, PRANK, preseq, pretext-suite, primalscheme, primer3, PrimerBLAST, PrimerPooler, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProtExcluder, protolite, PSASS, psmc, psutil, pullseq, purge_dups, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pymol-open-source, pyopencl, pypy, pyRAD, pyrho, Pyro4, pyseer, PySnpTools, python, PyTorch, PyVCF, qapa, qcat, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, quickmerge, QUMA, QuPath, R, RACA, racon, rad_haplotyper, RADIS, RadSex, RagTag, rapt, RAPTR-SV, RATT, raven, RAxML, raxml-ng, Ray, rck, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, Rebaler, reCOGnizer, Red, ReferenceSeeker, regenie, regtools, Relate, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, ReSeq, resistify, RevBayes, RFdiffusion, RFMix, RGAAT, rgdal, RGI, Rgtsvm, Ribotaper, ripgrep, rJava, rMATS, RNAMMER, rnaQUAST, Rnightlights, roadies, Roary, Rockhopper, rohan, RoseTTAFold-All-Atom, RoseTTAFold2NA, rphast, Rqtl, Rqtl2, RSAT, rseg, RSEM, RSeQC, RStudio, rtfbs_db, ruby, run_dbcan, rv-tdt, sabre, SaguaroGW, salmon, SALSA, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, SCALE, scanorama, SCE-VCF, scikit-learn, Scoary, scoary-2, scTE, scythe, seaborn, SEACR, SecretomeP, segul, self-assembling-manifold, selscan, seqfu, seqkit, SeqPrep, SeqSero2, seqtk, SequelTools, sequenceTubeMap, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, SHAPEIT5, shasta, Shiny, shoelaces, shore, SHOREmap, shortBRED, SHRiMP, SICER2, sickle, sift4g, SignalP, SimPhy, simuPOP, sina, SINGER, singularity, sinto, sirius, sistr_cmd, skani, SKESA, skewer, SLiM, SLURM, smap, smash, smcpp, smoove, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, snapatac2, SNAPP, SnapTools, snATAC, SNeP, Sniffles, snippy, snp-sites, snpArcher, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SoloTE, SomaticSniper, songbird, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, sparsehash, SPARTA, speedseq, split-fasta, SQANTI3, sqlite, SqueezeMeta, SQuIRE, SRA Toolkit, srst2, ssantichaivekin/empress, stacks, Stacks 2, stairway-plot, stampy, STAR, staramr, Starcode, statmodels, stellarscope, STITCH, STPGA, StrainPhlAn, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, Structure_threader, Struo2, stylegan2-ada-pytorch, subread, sumatra, supernova, suppa, SURPI, surpyvor, SURVIVOR, sutta, SV-plaudit, SVaBA, SVclone, SVDetect, svengine, SVseq2, svtools, svtyper, svviz2, SWAMP, sweed, SweepFinder, SweepFinder2, sweepsims, swiss2fasta.py, sword, syri, tabix, TAGADA, tagdust, Taiji, tama, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tax_myPHAGE, tbl2asn, tcoffee, TE-Aid, telescope, TELR, TensorFlow, TEToolkit, TEtranscripts, texlive, TFEA, tfmodisco, tfTarget, thermonucleotideBLAST, ThermoRawFileParser, TMHMM, tmux, Tomahawk, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, TRANSIT, transrate, TRAP, tree, treeCl, treemix, treePL, Trim Galore!, trimal, trimmomatic, Trinity, Trinotate, TrioCNV2, tRNAscan-SE, Trycycler, twisst2, UBCG2, UCSC Kent utilities, ullar, ultra, ultraplex, UMAP, UMI-tools, umi-transfer, UMIScripts, Unicycler, UniRep, unitig-caller, unrar, usearch, VALET, valor, vamb, variabel, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, VCF2PCACluster, vcf2phylip, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, verkko, VESPA, vg, Vicuna, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, visidata, vispr, VizBin, vmatch, vscode, vsearch, vt, WASP, webin-cli, wget, wgs-assembler (Celera), WGSassign, What_the_Phage, wiggletools, windowmasker, wine, Winnowmap, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha, yahs, yap
Details for bakta (If the copy-pasted commands do not work, use this tool to remove unwanted characters)
Name: | bakta |
Version: | 1.9.3 |
OS: | Linux |
About: | Annotation of bacterial genomes & plasmids |
Added: | 12/9/2020 10:35:26 AM |
Updated: | 5/8/2024 3:17:33 PM |
Link: | https://github.com/oschwengers/bakta |
Notes: | Launch the commands from your data directories.
1) run bakta command
singularity run --bind $PWD --pwd $PWD /programs/bakta-1.9.3/bakta.sif --help
2) run other commands in the backage
#bakta_db
singularity exec --bind $PWD --pwd $PWD /programs/bakta-1.9.3/bakta.sif bash -c "source /opt/conda/bashrc; bakta_db --help"
#amrfinder_update
singularity exec --bind $PWD --pwd $PWD /programs/bakta-1.9.3/bakta.sif bash -c "source /opt/conda/bashrc; amrfinder_update --help"
Instructions for running version 1.5.1 on Rocky 9 system (dependencies not installed)
# set up environment
export PYTHONPATH=/programs/bakta-1.5.1/lib64/python3.9/site-packages:/programs/bakta-1.5.1/lib/python3.9/site-packages
export PATH=/programs/bakta-1.5.1/bin:$PATH
# run command
bakta_db list
bakta --help
|
Notify me if this software is upgraded or changed [You need to be logged in to use this feature]