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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 491 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, ABruijn, ABySS, AdapterRemoval, Admixtools, Admixture, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, antiSMASH, apollo, Arlequin, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, AWS command line interface, axe, bamtools, Basset, BayeScan, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, bigQF, bigWig, 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, canu, CAP3, cBar, CBSU RNAseq, cd-hit, CEGMA, CellRanger, centrifuge, CFSAN SNP pipeline, CheckM, Circlator, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, copyNumberDiff, cortex_var, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, dDocent, DeconSeq, deepTools, delly, destruct, DETONATE, diamond, Discovar, Discovar de novo, distruct, Docker, dREG, dREG.HD, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, EDGE, EIGENSOFT, EMBOSS, entropy, ephem, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, fastcluster, FastML, fastp, fastq_species_detector, FastQC, fastStructure, FastTree, FASTX, fineRADstructure, fineSTRUCTURE, flash, flash2, Flexible Adapter Remover, FMAP, FragGeneScan, freebayes, FunGene Pipeline, GAEMR, GATK, gatk4, GBRS, gcc, GCTA, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, germline, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, gradle-4.4, 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, impute2, INDELseek, infernal, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, khmer, kSNP, kWIP, LACHESIS, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, 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, Migrate-n, mira, miRDeep2, MISO (misopy), MixMapper, MKTest, MMAP, MMSEQ, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, MUSIC, muTect, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, Novoalign, NovoalignCS, Oases, OBITools, Orthomcl, PacBioTestData, PAGIT, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pbalign, pbh5tools, PBJelly, PBSuite, PeakRanger, PeakSplitter, PEAR, PennCNV, PfamScan, PGDSpider, ph5tools, Phage_Finder, PHAST, PHRAPL, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, Plotly, popbam, prinseq, prodigal, progressiveCactus, prokka, pyani, 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, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, selscan, Sentieon, SeqPrep, sgrep, sgrep sorted_grep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, sistr_cmd, skewer, SLiM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SNAPP, snATAC, SNeP, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, SPAdes, SparCC, SRA Toolkit, srst2, stacks, Stacks 2, stampy, STAR, statmodels, STITCH, STPGA, 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, TopHat, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMI-tools, Unicycler, unrar, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, Velvet, VESPA, ViennaRNA, VIP, VirSorter, VirusDetect, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for GeneMark (hide)

Name:GeneMark
Version:4.30
OS:Linux
About:This program combines GeneMark.hmm (prokaryotic) and GeneMark (prokaryotic) with a self-training procedure that determines parameters of the models of both GeneMark.hmm and GeneMark.
Added:12/6/2013 2:00:50 PM
Updated:3/26/2016 8:36:42 AM
Link:http://topaz.gatech.edu/background.html
Notes:

For the new version of genemark suite, please download the software suite and key file from the website http://exon.gatech.edu/genemark/license_download.cgi. It requires you to fill out the agreement form and put key file in your home directory (~/.gm_key).

 


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