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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 Variant Effect Predictor (hide)

Name:Variant Effect Predictor
Version:77
OS:Linux
About:Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Added:10/13/2014 4:34:06 PM
Updated:
Link:http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
Notes:

Installed on cbsumm01. Use:

/local/vep/variant_effect_predictor.pl [options]

All available data files (both vep, and fasta) are cached locally in /local/vep-cache , here is the list:

1 : ailuropoda_melanoleuca_vep_77_ailMel1
2 : anas_platyrhynchos_vep_77_BGI_duck_1.0
3 : anolis_carolinensis_vep_77_AnoCar2.0
4 : astyanax_mexicanus_vep_77_AstMex102
5 : bos_taurus_vep_77_UMD3.1
6 : caenorhabditis_elegans_vep_77_WBcel235
7 : callithrix_jacchus_vep_77_C_jacchus3.2.1
8 : canis_familiaris_vep_77_CanFam3.1
9 : cavia_porcellus_vep_77_cavPor3
10 : chlorocebus_sabaeus_vep_77_ChlSab1.1
11 : choloepus_hoffmanni_vep_77_choHof1
12 : ciona_intestinalis_vep_77_KH
13 : ciona_savignyi_vep_77_CSAV2.0
14 : danio_rerio_merged_vep_77_Zv9
15 : danio_rerio_refseq_vep_77_Zv9
16 : danio_rerio_vep_77_Zv9
17 : dasypus_novemcinctus_vep_77_Dasnov3.0
18 : dipodomys_ordii_vep_77_dipOrd1
19 : drosophila_melanogaster_vep_77_BDGP5
20 : echinops_telfairi_vep_77_TENREC
21 : equus_caballus_vep_77_EquCab2
22 : erinaceus_europaeus_vep_77_HEDGEHOG
23 : felis_catus_vep_77_Felis_catus_6.2
24 : ficedula_albicollis_vep_77_FicAlb_1.4
25 : gadus_morhua_vep_77_gadMor1
26 : gallus_gallus_merged_vep_77_Galgal4
27 : gallus_gallus_refseq_vep_77_Galgal4
28 : gallus_gallus_vep_77_Galgal4
29 : gasterosteus_aculeatus_vep_77_BROADS1
30 : gorilla_gorilla_vep_77_gorGor3.1
32 : homo_sapiens_merged_vep_77_GRCh38
34 : homo_sapiens_refseq_vep_77_GRCh38
36 : homo_sapiens_vep_77_GRCh38
37 : ictidomys_tridecemlineatus_vep_77_spetri2
38 : latimeria_chalumnae_vep_77_LatCha1
39 : lepisosteus_oculatus_vep_77_LepOcu1
40 : loxodonta_africana_vep_77_loxAfr3
41 : macaca_mulatta_vep_77_MMUL_1
42 : macropus_eugenii_vep_77_Meug_1.0
43 : meleagris_gallopavo_vep_77_UMD2
44 : microcebus_murinus_vep_77_micMur1
45 : monodelphis_domestica_vep_77_BROADO5
46 : mus_musculus_merged_vep_77_GRCm38
47 : mus_musculus_refseq_vep_77_GRCm38
48 : mus_musculus_vep_77_GRCm38
49 : mustela_putorius_furo_vep_77_MusPutFur1.0
50 : myotis_lucifugus_vep_77_Myoluc2.0
51 : nomascus_leucogenys_vep_77_Nleu1.0
52 : ochotona_princeps_vep_77_pika
53 : oreochromis_niloticus_vep_77_Orenil1.0
54 : ornithorhynchus_anatinus_vep_77_OANA5
55 : oryctolagus_cuniculus_vep_77_OryCun2.0
56 : oryzias_latipes_vep_77_MEDAKA1
57 : otolemur_garnettii_vep_77_OtoGar3
58 : ovis_aries_vep_77_Oar_v3.1
59 : pan_troglodytes_vep_77_CHIMP2.1.4
60 : papio_anubis_vep_77_PapAnu2.0
61 : pelodiscus_sinensis_vep_77_PelSin_1.0
62 : petromyzon_marinus_vep_77_Pmarinus_7.0
63 : poecilia_formosa_vep_77_PoeFor_5.1.2
64 : pongo_abelii_vep_77_PPYG2
65 : procavia_capensis_vep_77_proCap1
66 : pteropus_vampyrus_vep_77_pteVam1
67 : rattus_norvegicus_merged_vep_77_Rnor_5.0
68 : rattus_norvegicus_refseq_vep_77_Rnor_5.0
69 : rattus_norvegicus_vep_77_Rnor_5.0
70 : saccharomyces_cerevisiae_vep_77_R64-1-1
71 : sarcophilus_harrisii_vep_77_DEVIL7.0
72 : sorex_araneus_vep_77_COMMON_SHREW1
73 : sus_scrofa_merged_vep_77_Sscrofa10.2
74 : sus_scrofa_refseq_vep_77_Sscrofa10.2
75 : sus_scrofa_vep_77_Sscrofa10.2
76 : taeniopygia_guttata_vep_77_taeGut3.2.4
77 : takifugu_rubripes_vep_77_FUGU4
78 : tarsius_syrichta_vep_77_tarSyr1
79 : tetraodon_nigroviridis_vep_77_TETRAODON8
80 : tupaia_belangeri_vep_77_TREESHREW
81 : tursiops_truncatus_vep_77_turTru1
82 : vicugna_pacos_vep_77_vicPac1
83 : xenopus_tropicalis_vep_77_JGI_4.2
84 : xiphophorus_maculatus_vep_77_Xipmac4.4.2
85: vitis_vinifera_vep_23
 


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