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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 545 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, Admixtools, Admixture, agrep, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, antiSMASH, apollo, Arlequin, aspera, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, AWS command line interface, axe, bamtools, Basset, BayeScan, Bayescenv, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, bigQF, bigWig, bioawk, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, BMGE, bmtagger, Boost, Bowtie, Bowtie2, BPGA, BreedingSchemeLanguage, breseq, BSseeker2, BUSCO, BWA, bwa-meth, cactus, canu, CAP3, cBar, CBSU RNAseq, CCTpack, cd-hit, CEGMA, CellRanger, centrifuge, CFSAN SNP pipeline, CheckM, chromosomer, Circlator, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, copyNumberDiff, cortex_var, CRISPRCasFinder, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, dDocent, DeconSeq, deepTools, defusion, delly, destruct, DETONATE, diamond, Discovar, Discovar de novo, distruct, Docker, dREG, dREG.HD, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, ectyper, EDGE, edirect, EIGENSOFT, EMBOSS, entropy, ephem, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, fastcluster, FastML, fastp, fastq_species_detector, FastQC, fastsimcoal26, fastStructure, FastTree, FASTX, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, freebayes, FunGene Pipeline, GAEMR, Galaxy, GATK, gatk4, GBRS, gcc, GCTA, gdc-client, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, germline, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, gradle-4.4, graftM, graphviz, Grinder, GROMACS, GSEA, Gubbins, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, HiC-Pro, HiCExplorer, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, HUMAnN2, hyperopt, HyPhy, iAssembler, IBDLD, IDBA-UD, IDP-denovo, IgBLAST, IGV, IMa2, IMa2p, IMAGE, ImageJ, impute2, IMSA-A, INDELseek, infernal, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, keras, khmer, KmerFinder, kraken, kSNP, kWIP, LACHESIS, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, Lighter, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, lyve-SET, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, MaxBin, mccortex, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mira, miRDeep2, MISO (misopy), MITObim, MixMapper, MKTest, MMAP, MMSEQ, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, MUSIC, muTect, Nanopolish, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, NLR-Parser, Novoalign, NovoalignCS, nvidia-docker, Oases, OBITools, Orthomcl, PacBioTestData, PAGIT, paleomix, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pbalign, pbh5tools, PBJelly, PBSuite, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, PfamScan, PGDSpider, ph5tools, Phage_Finder, PHAST, PHRAPL, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, Plotly, popbam, Porechop, prinseq, prodigal, progressiveCactus, prokka, psutil, pyani, PyCogent, pyfaidx, pyGenomeTracks, PyMC, pyRAD, Pyro4, PySnpTools, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RAPTR-SV, RAxML, Ray, Rcorrector, RDP Classifier, REAPR, RepeatMasker, RepeatModeler, RFMix, RGI, ripgrep, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, salmon, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, selscan, Sentieon, SeqPrep, seqtk, Seurat, sgrep, sgrep sorted_grep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, singularity, sistr_cmd, SKESA, skewer, SLiM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SNAPP, snATAC, SNeP, snippy, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, SPAdes, SparCC, SPARTA, SRA Toolkit, srst2, stacks, Stacks 2, stairway-plot, stampy, STAR, Starcode, statmodels, STITCH, STPGA, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, supernova, SURPI, sutta, SVDetect, svtools, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TASSEL 3, TASSEL 4, TASSEL 5, tcoffee, TensorFlow, TEToolkit, TMHMM, tmux, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMAP, UMI-tools, Unicycler, unrar, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, Velvet, VESPA, vg, ViennaRNA, VIP, VirSorter, VirusDetect, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for VirusFinder 2 (hide)

Name:VirusFinder 2
Version:2.0
OS:Linux
About:Tool for characterizing intra-host viruses through next generation sequencing (NGS) data.
Added:9/2/2014 5:40:16 PM
Updated:
Link:https://bioinfo.uth.edu/VirusFinder/
Notes:You need to use full path to the binaries:

/programs/VirusFinder2.0/VirusFinder.pl [options]

You can also add the program to your PATH:

export PATH=/programs/VirusFinder2.0:$PATH

and then use it directly by typing program name at the prompt.

Virus sequences database is stored in /shared_data/VirusFinder, but it MUST be copied to /workdir before using it:

cp -R /shared_data/VirusFinder /workdir

A sample config.txt configured for BioHPC Lab is in /programs/VirusFinder2.0 - you will need to copy it to your working directory and modify as needed for your computations (see VirusFinder documentation).


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