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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 569 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, atac-seq-pipeline, 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, bgen, 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, Conda, copyNumberDiff, cortex_var, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, dDocent, DeconSeq, deepTools, defusion, delly, destruct, DETONATE, diamond, diploSHIC, Discovar, Discovar de novo, distruct, DIYABC, Docker, dREG, dREG.HD, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, ectyper, EDGE, edirect, eems, 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, gffread, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, gradle-4.4, graftM, graphviz, Grinder, GROMACS, GSEA, GTFtools, 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, IGoR, 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, mcl, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, Minimac4, 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, plink2, Plotly, popbam, Porechop, portcullis, prinseq, prodigal, progressiveCactus, prokka, psutil, pyani, PyCogent, pyfaidx, pyGenomeTracks, PyMC, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RadSex, RAPTR-SV, RAxML, Ray, Rcorrector, RDP Classifier, REAPR, Relate, RepeatMasker, RepeatModeler, RFMix, RGI, Rgtsvm, ripgrep, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, salmon, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, seaborn, 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, vdjtools, Velvet, vep, VESPA, vg, ViennaRNA, VIP, VirSorter, VirusDetect, VirusFinder 2, VizBin, vmatch, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for BEDtools (hide)

Name:BEDtools
Version:bedtools-2.27.1
OS:Linux
About:BED file operation.
Added:2/6/2012 9:23:52 AM
Updated:5/8/2018 2:40:38 PM
Link:http://bedtools.readthedocs.io/en/latest/index.html
Manual:http://bedtools.readthedocs.io/en/latest/
Download:http://bedtools.readthedocs.io/en/latest/content/installation.html
Platform:all
Notes:The latest version of the program is in your PATH, and can be used directly by typing its name at the prompt:

[prog] [options]
(where [prog] is one of BEDtools programs)

There are 5 previous version(s) available. Any version can be accessed either by typing full path, or by adding it to the PATH and then typing its name at the prompt. NOTE: you need to set PATH only once per login/session.
versionaccess
bedtools-2.27.1
(latest)
full path:/programs/bedtools-2.27.1/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools-2.27.1/bin:$PATH
2.26.0
full path:/programs/bedtools2-2.26.0/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools2-2.26.0/bin:$PATH
2.25.0
full path:/programs/bedtools2-2.25.0/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools2-2.25.0/bin:$PATH
2.22.1
full path:/programs/bedtools2-2.22.1/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools2-2.22.1/bin:$PATH
2.19.1
full path:/programs/bedtools2-2.19.1/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools2-2.19.1/bin:$PATH
2.17.0
full path:/programs/bedtools-2.17.0/bin/[prog] [options]
add to PATH:export PATH=/programs/bedtools-2.17.0/bin:$PATH


If you have used bedtools before, please be aware that version 2.2 and later change the -a -b definiton for some function.

for example:

old command: bedtools coverage -abam my.bam -b my.bed

new command: bedtools coverage -a my.bed -b my.bam

There is no need to use "abam" to define bam file, as bedtools can detect format by itself 

 


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