BioHPC Cloud Software
There are 1359 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, AFsample2, AGAT, agrep, albacore, Alder, AliTV-Perl interface, AlleleSeq, ALLMAPS, ALLPATHS-LG, alphafast, Alphafold, Alphafold3, alphapickle, Alphapulldown, AlphScore, Amber, AMOS, AMPHORA, amplicon.py, AMRFinder, AMRplusplus, analysis, ANGSD, AnnotaPipeline, Annovar, ant, antiSMASH, ANTs, anvio, apollo, arcs, ARGweaver, aria2, ariba, ARIES, 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, bactopia, BactSNP, bakta, BAMdash, bamm, bamsnap, bamsurgeon, bamtools, bamUtil, barcode_splitter, BarNone, Basset, BayeScan, Bayescenv, bayesR, baypass, bazel, BBMap/BBTools, bcalm, 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, bioinfo-notebook, biom-format, BioPerl, BioPython, Birdsuite, biscuit, Bismark, Blackbird, blasr, BLAST, BLAST_to_BED, blast2go, BLAT, BlobToolKit, BLUPF90, BMGE, bmtagger, boltz, bonito, Boost, Bowtie, Bowtie2, BPGA, bpnet-lite, Bracken, BRAKER, BRAT-NextGen, BRBseqTools, BreedingSchemeLanguage, breseq, brisktyper, brocc, BSBolt, bsmap, BSseeker2, btyper3, bubblewrap, BUSCO, BUSCO Phylogenomics, BWA, bwa-mem2, bwa-meth, bwtool, cactus, CAFE, CAFE5, caffe, cagee, canu, Canvas, CAP3, caper, CarveMe, CAT, catastrophy, catch, cBar, CBSU RNAseq, CCMetagen, CCTpack, cd-hit, cdbfasta, cdo, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, cellsnp-lite, centrifuge, centrifuger, centroFlye, CFM-ID, CFSAN SNP pipeline, CGAT, CheckM, CheckM2, chimera, ChimeraTE, chimerax, chip-seq-pipeline, chromeister, ChromHMM, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, clam, claude code, Claude Science, ClermonTyping, CLImATHET, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, cNMF, CNVnator, codex, coidb, coinfinder, colabfold, COLMAP, CombFold, Comparative-Annotation-Toolkit, compat, CONCOCT, Conda, Conform-gt, conpair, Cooler, coolpuppy, cooltools, copyNumberDiff, cortex_var, CoverM, crabs, CRISPRCasFinder, CRISPResso, crispron, Cromwell, CrossMap, CRT, CSP2, csubst, cuda, Cufflinks, curatedMetagenomicDataTerminal, cutadapt, cuteFC, cuteSV, Cytoscape, czid, 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, distiller, 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, EagleC, earlgrey, ecCodes, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, egapx, eggnog-mapper, EIGENSOFT, elai, ElMaven, emacs, EMBLmyGFF3, EMBOSS, EMIRGE, Empress, emu, 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, FASTK, 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, FEELnc, feems, feh, FFmpeg, fgbio, ficle, figaro, Fiji, Filtlong, fineRADstructure, fineSTRUCTURE, FIt-SNE, FlaGs2, FLAME-python, flash, flash2, flexbar, Flexible Adapter Remover, flexidot, Flye, FMAP, foldmason, foldseek, foundry, FragGeneScan, FragGeneScan, FragPipe, FRANz, freebayes, FSA, funannotate, FunGene Pipeline, FunOMIC, G-PhoCS, g4predict, GADMA, GAEMR, Galaxy, Galaxy in Docker, garlic, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, gbsx, gcc, GCTA, GDAL, gdc-client, gedi, gem, GEM library, gemini-cli, GEMMA, GeMoMa, GENECONV, geneid, GeneMark, GeneRax, Genespace, GenoFLU, genomad, Genome STRiP, Genome Workbench, GenomeMapper, Genomescope, GenomeThreader, genometools, GenomicConsensus, genozip, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GetOrganelle, gfastats, gfaviz, GffCompare, gffread, giggle, gingr, git, glactools, GlimmerHMM, GLIMPSE, GLnexus, Globus connect personal, GMAP/GSNAP, gmx_MMPBSA, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GONE, GoShifter, gradle, GraffiTE, 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, HapHiC, HaploMerger, Haplomerger2, haplostrips, HaploSync, happ, HapSeq2, harpy, HarvestTools, haslr, hdf5, helixer, hget, hh-suite, HiC-Pro, hic_qc, HiCExplorer, hicstuff, HiFiAdapterFilt, hifiasm, hificnv, HiPhase, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, https://github.com/ksahlin/strobealign, huggingface-hub, 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, IRMA, isoseq, itsx, iva, ivar, JaBbA, jags, Jane, java, jbrowse, JCVI, jellyfish, jsalignon/cactus, juicer, julia, jupyter, jupyterlab, kaiju, kallisto, Kent Utilities, keras, khmer, kineticsTools, kinfin, king, kma, KMC, KmerFinder, KmerGenie, kneaddata, kraken, KrakenTools, KronaTools, kSNP, kWIP, LACHESIS, lammps, LAPACK, lapels, LAST, lastz, lcMLkin, LDAK, LDBlockShow, LDhat, LeafCutter, leeHom, lefse, lep-anchor, Lep-MAP3, LEVIATHAN, lftp, Liftoff, lifton, ligandmpnn, Lighter, LinkedSV, LINKS, localcolabfold, LocARNA, LocusZoom, lofreq, longcallR, longcallR-nn, longqc, 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, majiq, MAKER, manta, mapDamage, mapquik, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, MCHelper, mcl, MCscan, MCScanX, mdust, medaka, medusa, medusa2, megahit, MeGAMerge, MEGAN, meirlop, MELT, MEME Suite, MERLIN, merqury, meryl, MetaBAT, MetaBinner, MetaboAnalystR, MetaCache, MetaCRAST, metaCRISPR, metamaps, MetAMOS, MetaPathways, MetaPhlAn, metapop, metaron, MetaVelvet, MetaVelvet-SL, metaWRAP, methbat, methpipe, methylasso, 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, MLNe, mlst, MMAP, MMSEQ, MMseqs2, MMTK, MobileElementFinder, ModDotPlot, modeltest, MODIStsp-2.0.5, module, moments, momi, MoMI-G, mongo, mono, monocle3, morphographx, 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, NanoLyse, NanoPlot, Nanopolish, nanovar, ncbi_datasets, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, NextPolish2, nf-core, nf-core/rnaseq, nf-LO, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NGSNGS, ngsplot, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, NLRtracker, Novoalign, NovoalignCS, nQuire, NRSA, ntSynt, nucMACC, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, odgi, OMA, Oneflux, OpenBLAS, openmpi, openslide, openssl, ORFeus, ORFfinder, orthodb-clades, OrthoFinder, orthologr, Orthomcl, osfclient, pacbio, PacBioTestData, PAGIT, pairtools, pal2nal, paleomix, PAML, panacus, panaroo, pandas, pandaseq, pandoc, pangene, pankmer, PanPhlAn, PanPhlAn_pangenome_exporter, Panseq, pantools, paPAML, Parsnp, PASA, PASTEC, PAUP*, pauvre, pb-assembly, pb-CpG-tools, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, pbpigeon, PBSuite, pbsv, pbtk, PCAngsd, pcre, pcre2, PeakRanger, peaks2utr, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, pharokka, phasedibd, PHAST, phenopath, PhiSpy, 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, prodigy, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProteinMPNN, proteowizard, 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, q2-picrust2, qapa, qcat, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, quarTeT, 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, readtagger, REAGO, REAPR, Rebaler, reCOGnizer, Red, ReferenceSeeker, regenie, regtools, REINDEER, Relate, relion, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, ReSeq, resistify, RevBayes, RFdiffusion, RFDpoly, RFMix, RGAAT, rgdal, RGI, Rgtsvm, Ribotaper, ripgrep, rJava, rMATS, RNAMMER, rnaQUAST, Rnightlights, roadies, Roary, Rockhopper, rohan, RoseTTAFold-All-Atom, RoseTTAFold2, RoseTTAFold2NA, rphast, RpsbProc, Rqtl, Rqtl2, RSAT, rseg, RSEM, RSeQC, RStudio, rtfbs_db, ruby, run_dbcan, rust, rv-tdt, sabre, SaguaroGW, salmon, SALSA, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, sawfish, SCALE, scanorama, SCE-VCF, scikit-learn, Scoary, scoary-2, SCOTCH, 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, simsapiper, simuPOP, simuscop, sina, SINGER, singularity, sinto, sirius, sistr_cmd, skani, skera, SKESA, skewer, slamdunk, SLiM, SLURM, smap, smash, smcpp, smoove, SMRT Analysis, SMRT LINK, smudgeplot, 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, sourmash, spaceranger, SPAdes, SPALN, SparCC, sparsehash, SPARTA, SpeciesDetector, 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, swarm, 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, TEFLoN, telescope, TELR, TEMP2, 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, ullar, ultra, ultraplex, UMAP, UMI-tools, umi-transfer, UMIScripts, Unicycler, UniRep, unitig-caller, unrar, usearch, VALET, valor, vamb, VAPiD, variabel, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, VCF2PCACluster, vcf2phylip, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, verkko, VESPA, vg, VIBRANT, Vicuna, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, visidata, vispr, VizBin, vmatch, vscode, vsearch, vSNP3, vt, WASP, webin-cli, wget, wgs-assembler (Celera), WGSassign, What_the_Phage, whatshap, wiggletools, windowmasker, wine, Winnowmap, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha, yahs, yap
Details for bactopia (If the copy-pasted commands do not work, use this tool to remove unwanted characters)
| Name: | bactopia |
| Version: | 4 |
| OS: | Linux |
| About: | An end-to-end workflow Nextflow pipeline for bacterial genome analysis. |
| Added: | 8/12/2026 5:43:50 PM |
| Updated: | |
| Link: | https://bactopia.io/ |
| Notes: | To run bactopia, first load the proper nexflow module and set the environment:
modue load nextflow/26.04.6
mkdir -p /workdir/$HOME/bactopia
. /programs/bactopia/bactopia-env.sh
then run the program using the singularity profile, e.g.,
nextflow run bactopia/bactopia -profile test,singularity
The singularity images and data downloaded during the run will be stored within /workdir/$HOME/bactopia.
The actual work will be perfomed and output will be stored in the directory from which the run was submitted.
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