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BioHPC Lab:
User Guide

 


BioHPC Lab Software

There is 390 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, 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 Picard (hide)

Name:Picard
Version:2.9.0
OS:Linux
About:A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
Added:12/13/2011 2:49:53 PM
Updated:4/8/2017 12:14:37 PM
Link:http://broadinstitute.github.io/picard/
Download:https://github.com/broadinstitute/picard/releases
Platform:all
Notes:

#To get help:

java -jar /programs/picard-tools-2.8.2/picard.jar -h 
#To get help for a specific picard tool:
java -jar /programs/picard-tools-2.8.2/picard.jar ValidateSamFile -h

To run previous versions of picard (1.109):

java -jar /programs/bin/picard-tools/[prog] [options]


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