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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 IMSA-A (hide)

Name:IMSA-A
Version:20170727
OS:Linux
About: Integrated Metagenomic Sequence Analysis
Added:6/28/2018 3:17:16 PM
Updated:
Link:https://github.com/JeremyCoxBMI/IMSA-A
Notes:

You will need to install the software by yourself, as you will need to modify the configuration files according to your project.

1. Download and de-compress IMSA software to your home directory.

wget http://sourceforge.net/projects/arron-imsa/files/imsa_v2.tar

tar xvf imsa_v2.tar

2. Download IMSA-files and put to the imsa_v2 directory from the first step.

git clone https://github.com/JeremyCoxBMI/IMSA-A.git

cp IMSA-A/*  imsa_v2/

3. You will need to modify the config.py file. Following the manual at:

https://github.com/JeremyCoxBMI/IMSA-A/blob/master/IMSA%2BA_Detailed_Direction.pdf

 

All required software are already installed on BioHPC:

BLAST+, BLAT and BOWTIE2 are in default PATH. 

Oases: https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=28#c 

Velvet: https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=14#c 

Trinity: https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=33#c 

 


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