BioHPC Cloud:
: User Guide

BioHPC Cloud Software

There is 723 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.

454 gsAssembler or gsMapper, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, agrep, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, amplicon.py, analysis, ANGSD, Annovar, antiSMASH, apollo, Arlequin, aspera, assembly-stats, atac-seq-pipeline, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, AWS command line interface, axe, BactSNP, bam2fastx, bamtools, bamUtil, BarNone, Basset, BayeScan, Bayescenv, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beast2, bedops, BEDtools, bfc, bgc, bgen, bigQF, bigWig, bioawk, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, 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, CarveMe, cBar, CBSU RNAseq, CCTpack, cd-hit, cdbfasta, CEGMA, CellRanger, cellranger-atac, centrifuge, CFM-ID, CFSAN SNP pipeline, CheckM, chimera, chromosomer, Circlator, Circos, Circuitscape, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, Conda, copyNumberDiff, cortex_var, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, danpos, dDocent, DeconSeq, Deepbinner, deepTools, defusion, delly, DESMAN, destruct, DETONATE, diamond, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, Docker, dREG, dREG.HD, drep, Drop-seq, dropEst, dropSeqPipe, dsk, Dsuite, dTOX, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, eems, EgaCryptor, EGAD, EIGENSOFT, EMBOSS, entropy, ephem, epic2, ermineJ, ete3, 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, fastsimcoal26, fastStructure, FastTree, FASTX, feh, FFmpeg, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, freebayes, FunGene Pipeline, G-PhoCS, GAEMR, Galaxy, GATK, gatk4, gatk4amplicon.py, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, 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, graphviz, GRiD, Grinder, GROMACS, GSEA, GTDB-Tk, GTFtools, Gubbins, GUPPY, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, HiC-Pro, HiCExplorer, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, HUMAnN2, hyperopt, HyPhy, iAssembler, IBDLD, IDBA-UD, IDP-denovo, idr, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, IMSA-A, INDELseek, infernal, Infomap, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, java, jbrowse, JCVI, jellyfish, JoinMap, juicer, julia, jupyter, kallisto, Kent Utilities, keras, khmer, KmerFinder, kraken, kSNP, kWIP, LACHESIS, lammps, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, lftp, Lighter, 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, MAQ, MASH, mashtree, Mashtree, MaSuRCA, Mauve, MaxBin, mccortex, mcl, MCscan, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, MMseqs2, mono, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMmer, muscle, MUSIC, muTect, Nanopolish, ncftp, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, nf-core/rnaseq, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, Novoalign, NovoalignCS, NRSA, nvidia-docker, Oases, OBITools, OMA, OrthoFinder, Orthomcl, pacbio, PacBioTestData, PAGIT, paleomix, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pbmm2, PBSuite, PCAngsd, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyloPhlAn2, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, plink2, Plotly, popbam, PopCOGenT, Porechop, portcullis, pplacer, PRANK, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, PSASS, psutil, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pyopencl, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RadSex, RAPTR-SV, RAxML, raxml-ng, Ray, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, ReferenceSeeker, Relate, RelocaTE2, RepeatMasker, RepeatModeler, RFMix, rgdal, RGI, Rgtsvm, ripgrep, rJava, RNAMMER, rnaQUAST, Rnightlights, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, ruby, sabre, SaguaroGW, salmon, Sambamba, samblaster, sample, SampleTracker, Samtools, Satsuma, Satsuma2, scanorama, scikit-learn, Scoary, scythe, seaborn, SecretomeP, selscan, Sentieon, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, shasta, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, SimPhy, simuPOP, singularity, sistr_cmd, SKESA, skewer, SLiM, SLURM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, SNAPP, snATAC, SNeP, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, SPARTA, 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, SVDetect, SVseq2, svtools, SWAMP, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tbl2asn, tcoffee, TensorFlow, TEToolkit, texlive, tfTarget, ThermoRawFileParser, TMHMM, tmux, 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 CONCOCT (hide)

export PATH=/programs/Anaconda2/bin:$PATH
export LD_LIBRARY_PATH=/programs/Anaconda2/lib:$LD_LIBRARY_PATH
source activate concoct_env

##run tool
concoct
## run scripts
cut_up_fasta.py

source deactivate concoct_env