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BioHPC Cloud:
: User Guide

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BioHPC Cloud Software

There is 843 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, Cooler, 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, MODIStsp-2.0.5, 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, Point Cloud Library, 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 BUSCO (hide)

Name:BUSCO
Version:5.1.3
OS:Linux
About:Assessing genome assembly and annotation completeness.
Added:1/22/2016 4:41:55 PM
Updated:5/20/2021 4:15:01 PM
Link:http://busco.ezlab.org/#software
Notes:

#To run pre-installed version (5.1.2)

#set environment
source /programs/miniconda3/bin/activate busco-5.1.2

#run command
busco

 

# Two ways to install latest version of busco by yourself

1. use singularity (quick and easier)  check tag

#download and build image (replacing 5.1.3--pyhdfd78af_0 with latest tag)
singularity pull busco_5.1.3.sif docker://quay.io/biocontainers/busco:5.1.3--pyhdfd78af_0

#run command
./busco_5.1.3.sif busco -h

2. use conda (very slow) check version

#create conda environment
source $HOME/miniconda3/bin/activate
conda create -n busco -c bioconda -c conda-forge busco=5.1.3

#run busco
conda activate busco
#run command
busco -h 

# follow instructions on this page to run busco

https://busco.ezlab.org/busco_userguide.html#running-busco

 


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