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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 840 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-dna, 454 gsAssembler or gsMapper, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, agrep, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, amplicon.py, AMRFinder, analysis, ANGSD, Annovar, antiSMASH, anvio, apollo, arcs, ARGweaver, Arlequin, ART, aspera, assembly-stats, ASTRAL, atac-seq-pipeline, ataqv, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, atom, ATSAS, Augustus, AWS command line interface, AWS v2 Command Line Interface, axe, axel, BactSNP, bakta, bam2fastx, bamtools, bamUtil, BarNone, Basset, BayeScan, Bayescenv, baypass, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beast2, bedops, BEDtools, bfc, bgc, bgen, bigQF, bigWig, bioawk, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, BLAST_to_BED, blast2go, BLAT, BLUPF90, BMGE, bmtagger, Boost, Bowtie, Bowtie2, BPGA, Bracken, BRAKER, BRAT-NextGen, BreedingSchemeLanguage, breseq, brocc, BSseeker2, BUSCO, BWA, bwa-meth, cactus, CAFE, canu, CAP3, caper, CarveMe, cBar, CBSU RNAseq, CCTpack, cd-hit, cdbfasta, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, centrifuge, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, chimera, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, Conda, copyNumberDiff, cortex_var, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, cuteSV, dadi, dadi-1.6.3_modif, danpos, dDocent, DeconSeq, Deepbinner, DeepTE, deepTools, defusion, delly, DESMAN, destruct, DETONATE, diamond, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, Docker, dREG, dREG.HD, drep, drive, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, dynare, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, EIGENSOFT, EMBOSS, Empress, entropy, epa-ng, ephem, epic2, ermineJ, ete3, EVM, exabayes, exonerate, ExpansionHunterDenovo-v0.8.0, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastANI, fastcluster, FastME, FastML, fastp, FastQ Screen, fastq_pair, fastq_species_detector, FastQC, fastqsplitter, fastsimcoal26, fastStructure, FastTree, FASTX, feh, FFmpeg, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, freebayes, FSA, FunGene Pipeline, G-PhoCS, GADMA, GAEMR, Galaxy in Docker, Galaxy Server, GATK, gatk4, gatk4amplicon.py, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, GENECONV, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomeThreader, genometools, GenomicConsensus, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GffCompare, gffread, giggle, glactools, GlimmerHMM, GMAP/GSNAP, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GoShifter, gradle-4.4, graftM, GraPhlAn, graphviz, GRiD, Grinder, GROMACS, GSEA, gsort, GTDB-Tk, GTFtools, Gubbins, GUPPY, hail, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, haslr, hdf5, hget, hh-suite, HiC-Pro, HiCExplorer, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, HUMAnN2, hyperopt, HyPhy, iAssembler, IBDLD, idba, IDBA-UD, IDP-denovo, idr, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, IMSA-A, INDELseek, infernal, Infomap, InStruct, Intel MKL, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, Jane, java, jbrowse, JCVI, jellyfish, JoinMap, juicer, julia, jupyter, kallisto, Kent Utilities, keras, khmer, kinfin, king, KmerFinder, KmerGenie, kraken, kSNP, kWIP, LACHESIS, lammps, LAST, lcMLkin, LDAK, leeHom, lep-anchor, Lep-MAP3, lftp, Lighter, LinkedSV, LINKS, LocARNA, LocusZoom, lofreq, longranger, LS-GKM, LTR_retriever, LUCY, LUCY2, LUMPY, lyve-SET, MACE, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, magick, MAKER, mapDamage, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Mauve, MaxBin, McClintock, mccortex, mcl, MCscan, MCScanX, medusa, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, metaron, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, MinCED, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, MMseqs2, MMTK, modeltest, module, moments, mono, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMandCo, MUMmer, muscle, MUSIC, Mutation-Simulator, muTect, MZmine, nag-compiler, nanofilt, Nanopolish, ncftp, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, nf-core/rnaseq, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, Novoalign, NovoalignCS, nQuire, NRSA, nvidia-docker, Oases, OBITools, Octave, OMA, openmpi, OrthoFinder, orthologr, Orthomcl, pacbio, PacBioTestData, PAGIT, paleomix, PAML, panaroo, pandas, pandaseq, pandoc, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, PBSuite, PCAngsd, pcre, pcre2, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, peppro, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyloPhlAn2, phylophlan3, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, platanus, Platypus, plink, plink2, Plotly, popbam, PopCOGenT, PopLDdecay, Porechop, poretools, portcullis, pplacer, PRANK, preseq, primalscheme, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProtExcluder, protolite, PSASS, psmc, psutil, purge_dups, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pyopencl, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, quickmerge, QUMA, R, RACA, racon, RADIS, RadSex, rapt, RAPTR-SV, RATT, RAxML, raxml-ng, Ray, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, Red, ReferenceSeeker, regenie, Relate, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, RFMix, RGAAT, rgdal, RGI, Rgtsvm, ripgrep, rJava, RNAMMER, rnaQUAST, Rnightlights, Roary, Rockhopper, rphast, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, ruby, sabre, SaguaroGW, salmon, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, SCALE, scanorama, scikit-learn, Scoary, scythe, seaborn, SecretomeP, selscan, Sentieon, seqkit, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, shasta, Shiny, shore, SHOREmap, shortBRED, SHRiMP, sickle, sift4g, SignalP, SimPhy, simuPOP, singularity, sinto, sistr_cmd, SKESA, skewer, SLiM, SLURM, smcpp, smoove, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, SNAPP, snATAC, SNeP, Sniffles, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, SPARTA, sqlite, SRA Toolkit, srst2, stacks, Stacks 2, stairway-plot, stampy, STAR, Starcode, statmodels, STITCH, STPGA, StrainPhlAn, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, Structure_threader, supernova, SURPI, sutta, SV-plaudit, SVDetect, SVseq2, svtools, svtyper, SWAMP, SweepFinder, SweepFinder2, sweepsims, tabix, Taiji, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tbl2asn, tcoffee, TensorFlow, TEToolkit, TEtranscripts, texlive, tfTarget, ThermoRawFileParser, TMHMM, tmux, Tomahawk, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, TRANSIT, transrate, TRAP, treeCl, treemix, Trim Galore!, trimal, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMAP, UMI-tools, Unicycler, UniRep, unrar, usearch, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, VESPA, vg, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, VizBin, vmatch, vsearch, vt, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for module (hide)

Name:module
Version:3.2.10
OS:Linux
About:set Environment Modules
Added:5/23/2021 5:30:01 PM
Updated:
Link:https://modules.readthedocs.io/en/latest/modulefile.html
Notes:

The module function only support a subset of BioHPC software. For most software, please use our software page.

Supported functions:

module avail                                   # List available modules

module avail R                                # List available "R" modules

module load          # load a module

module unload     # unload a module

module list           # List loaded modules

module switch newModule

 


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