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BioHPC Lab:
User Guide

 


BioHPC Lab Software

There is 391 software titles installed in BioHPC Lab. 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 Lab.

454 gsAssembler or gsMapper, a5, ABruijn, ABySS, AdapterRemoval, Admixtools, Admixture, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, apollo, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, bamtools, Basset, BayeScan, BBmap, BCFtools, bcl2fastq, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, biobambam, Bioconductor, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, bmtagger, Boost, Bowtie, Bowtie2, breseq, BSseeker2, BUSCO, BWA, canu, CAP3, CBSU RNAseq, cd-hit, CEGMA, CellRanger, CheckM, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, 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, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, EDGE, EIGENSOFT, EMBOSS, entropy, ermineJ, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastML, fastq_species_detector, FastQC, fastStructure, FastTree, FASTX, fineSTRUCTURE, flash, Flexible Adapter Remover, FMAP, freebayes, FunGene Pipeline, GATK, GBRS, GCTA, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, germline, GMAP/GSNAP, GNU Compilers, GNU parallel, Grinder, GROMACS, Gubbins, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HiC-Pro, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, HUMAnN2, HyPhy, iAssembler, IBDLD, IDBA-UD, IGV, IMa2, IMa2p, IMAGE, impute2, infernal, InStruct, InteMAP, InterProScan, iRep, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent source utilities, khmer, LACHESIS, lcMLkin, LDAK, leeHom, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, MACS, MaCS simulator, MACS2, MAFFT, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, mccortex, megahit, MEGAN, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, Migrate-n, mira, miRDeep2, MISO (misopy), MixMapper, MKTest, MMSEQ, mothur, MrBayes, mrsFAST, msld, MSMC, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, muTect, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, Novoalign, NovoalignCS, Oases, OBITools, Orthomcl, PAGIT, PAML, pandas, pandaseq, Panseq, PASA, PASTEC, pbalign, pbh5tools, PBJelly, PBSuite, PeakSplitter, PEAR, PennCNV, ph5tools, Phage_Finder, PHAST, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, Pindel, piPipes, PIQ, Platypus, plink, Plotly, popbam, prinseq, prodigal, progressiveCactus, prokka, pyRAD, PySnpTools, PyVCF, QIIME, QIIME2 q2cli, Quake, QuantiSNP2, QUAST, QUMA, R, RACA, RADIS, RAPTR-SV, RAxML, Ray, Rcorrector, REAPR, RepeatMasker, RepeatModeler, RFMix, RNAMMER, rnaQUAST, Roary, RSEM, RSeQC, RStudio, sabre, SaguaroGW, samblaster, Samtools, Satsuma, scikit-learn, scythe, Sentieon, SeqPrep, sgrep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, skewer, smcpp, SMRT Analysis, snakemake, snap, SNAPP, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, SPAdes, SRA Toolkit, srst2, stacks, stampy, STAR, statmodels, Strelka, 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, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, Velvet, VESPA, ViennaRNA, VIP, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for Trinity (hide)

Name:Trinity
Version:2.4.0
OS:Linux
About:De novo transcriptome assembly.
Added:12/13/2011 3:22:56 PM
Updated:5/29/2017 12:15:17 PM
Link:http://trinityrnaseq.github.io/
Notes:You need to use full path to the binaries:

/programs/trinityrnaseq-Trinity-v2.4.0/Trinity [options]

You can also add the program to your PATH:

export PATH=/programs/trinityrnaseq-Trinity-v2.4.0:$PATH

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

It is recommended to run on medium memory nodes (e.g., cbsumm03). A large memory machines (e.g. cbsulm05) may be needed to process larger datasets.

To lauch Trinity, use the full path to the executable, like so:

/programs/trinityrnaseq-Trinity-v2.4.0/Trinity [options] >& trinity.log &

If you wish to use eXpress software to estimake read abundance via Trinity's utility align_and_estimate_abundance.pl, add the location of the eXpress executable to the PATH:

export PATH=/programs/express:$PATH

TransDecoder is not part of Trinity release starting from 2.1.1.

Here is the instruction of running TransDecoder on BioHPC Lab:  https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=209#c 

 

There are 13 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
2.4.0
(latest)
full path:/programs/trinityrnaseq-Trinity-v2.4.0/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq-Trinity-v2.4.0:$PATH
2.3.2
full path:/programs/trinityrnaseq-2.3.2/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq-2.3.2:$PATH
2.2.0
full path:/programs/trinityrnaseq-2.2.0/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq-2.2.0:$PATH
2.1.1
full path:/programs/trinityrnaseq-2.1.1/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq-2.1.1:$PATH
2.0.4
full path:/programs/trinityrnaseq-2.0.4/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq-2.0.4:$PATH
20140413p1
full path:/programs/trinityrnaseq_r20140413p1/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r20140413p1:$PATH
r20131110
full path:/programs/trinityrnaseq_r20131110/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r20131110:$PATH
2013-02-25
full path:/programs/trinityrnaseq_r2013-02-25/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2013-02-25:$PATH
2013-02-16
full path:/programs/trinityrnaseq_r2013-02-16/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2013-02-16:$PATH
2012-10-05
full path:/programs/trinityrnaseq_r2012-10-05/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2012-10-05:$PATH
2012-06-08
full path:/programs/trinityrnaseq_r2012-06-08/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2012-06-08:$PATH
2012-04-27
full path:/programs/trinityrnaseq_r2012-04-27/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2012-04-27:$PATH
2011-11-26
full path:/programs/trinityrnaseq_r2011-11-26/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2011-11-26:$PATH
2011-08-20
full path:/programs/trinityrnaseq_r2011-08-20/Trinity [options]
add to PATH:export PATH=/programs/trinityrnaseq_r2011-08-20:$PATH



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