institute of biotechnology >> brc >> bioinformatics >> internal >> biohpc lab: user guide
 

BioHPC Lab:
User Guide

 


BioHPC Lab Software

There is 421 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, Arlequin, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, bamtools, Basset, BayeScan, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, biobambam, Bioconductor, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, bmtagger, Boost, Bowtie, Bowtie2, BPGA, breseq, BSseeker2, BUSCO, BWA, canu, CAP3, cBar, 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, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, fastcluster, FastML, fastq_species_detector, FastQC, fastStructure, FastTree, FASTX, fineSTRUCTURE, flash, Flexible Adapter Remover, FMAP, FragGeneScan, freebayes, FunGene Pipeline, GAEMR, 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, IgBLAST, IGV, IMa2, IMa2p, IMAGE, impute2, INDELseek, infernal, InStruct, InteMAP, InterProScan, iRep, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, khmer, LACHESIS, lcMLkin, LDAK, leeHom, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, MACS, MaCS simulator, MACS2, MAFFT, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, MaxBin, 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, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, MUSIC, 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, PeakRanger, PeakSplitter, PEAR, PennCNV, PGDSpider, ph5tools, Phage_Finder, PHAST, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, Pindel, piPipes, PIQ, Platypus, plink, Plotly, popbam, prinseq, prodigal, progressiveCactus, prokka, pyRAD, Pyro4, PySnpTools, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, QuantiSNP2, QUAST, QUMA, R, RACA, RADIS, RAPTR-SV, RAxML, Ray, Rcorrector, RDP Classifier, REAPR, RepeatMasker, RepeatModeler, RFMix, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, sabre, SaguaroGW, samblaster, Samtools, Satsuma, Satsuma2, scikit-learn, scythe, selscan, Sentieon, SeqPrep, sgrep, sgrep sorted_grep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, skewer, SLiM, smcpp, SMRT Analysis, snakemake, snap, SNAPP, SNeP, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, SPAdes, SRA Toolkit, srst2, stacks, stampy, STAR, statmodels, STITCH, 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, VirusDetect, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for BUSCO (hide)

Name:BUSCO
Version:3.0.2
OS:Linux
About:Assessing genome assembly and annotation completeness.
Added:1/22/2016 4:41:55 PM
Updated:10/25/2017 9:11:13 PM
Link:http://busco.ezlab.org/#software
Notes:

Here are the steps to run busco on the sample data coming with the software(/programs/busco-3.0.2/sample_data).

Replace XXXX with your BioHPC user ID. . 

 

### Step 1. Prepare the data files and species profile.  In this example, we use the data coming with the software. To run busco on your real data, replace "target.fa" with your genome fasta file, replace "example" directory with the appropriate profile directory from http://busco.ezlab.org/

cd /workdir/XXXX

cp -r /programs/busco-3.0.2/sample_data/example ./

cp  /programs/busco-3.0.2/sample_data/target.fa ./

 

### Step 2. Make a local copy of the config files for BUSCO and AUGUSTUS

cp /programs/busco-3.0.2/config/config.ini  ./
cp -r /programs/augustus-3.3/config ./

export AUGUSTUS_CONFIG_PATH=/workdir/XXXX//config

export BUSCO_CONFIG_FILE="/workdir/XXXX/config.ini"

 

### Step 3. Set up the path

export PYTHONPATH=/programs/busco-3.0.2/lib/python3.6/site-packages
export PATH=/programs/busco-3.0.2/scripts:/programs/augustus-3.3/bin:/programs/augustus-3.3/scripts:$PATH

 

### Step 4. Run the code (check manual for description of all parameters http://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf )

run_BUSCO.py --in ./target.fa --lineage_path ./example --mode genome --out SAMPLE --cpu 8

 

### The following code generate a summary plot of one or multiple genomes

create a directory busco_summary/, and copy the short_summary_xxxxxx.txt file of all assemblies into the directory.

If it is a new ssh session, you will need to set the environment again:

export PYTHONPATH=/programs/busco-3.0.2/lib/python3.6/site-packages

 

/programs/busco-3.0.2/scripts/generate_plot.py -wd busco_summary

 

################################

Instruction to run 2.0:

Here are the steps to run busco on the sample data coming with the software(/programs/BUSCO_v1.1b1/sample_data).

Replace XXXX with your BioHPC user ID. To run busco on your real data, replace "/programs/BUSCO_v2.0/sample_data/target.fa" with your genome fasta file, replace "/programs/BUSCO_v2.0/sample_data/example" with the appropriate profile directory from http://busco.ezlab.org/ . 

cd /workdir/XXXX

cp -r /programs/BUSCO_v2.0/sample_data/example ./

cp  /programs/BUSCO_v2.0/sample_data/target.fa ./

cp -r /programs/augustus-3.2.1 ./

export AUGUSTUS_CONFIG_PATH=/workdir/XXXX/augustus-3.2.1/config

export PATH=/programs/hmmer/binaries:/programs/emboss/bin:$PATH

export PATH=/workdir/XXXX/augustus-3.2.1/scripts:/workdir/XXXX/augustus-3.2.1/bin:$PATH

python3 /programs/BUSCO_v2.0/BUSCO.py -o SAMPLE -i target.fa -l example -m genome


Notify me if this software is upgraded or changed [You need to be logged in to use this feature]

 

Website credentials: login  Web Accessibility Help