Software

Software installed on the clusters is available for public use without restriction.  Users must be comfortable in a Unix environment and understand how to properly submit jobs.  The Xanadu cluster is replacing the BBC cluster for research use.  Request additional information, accounts, and software installs for Xanadu here.

Software Name Version Executable (case-senstitive, ‘:’ means multiple options; “module load …”)
BBC Xanadu (CAM account)

Sequence Alignment/Annotation

Augustus 3.2.3 module load Augustus
augustus
BARRNAP 0.6 module load Barnap
barrnap
module load barnap
barnap
BEDtools 2.26.0 module load Bedtools
bedtools
Blat 36×2 module load Blat
blat
Busco 3.0.2b module load BUSCO_v2.0

module load busco/3.0.2b

CEGMA 2.5 module load CEGMA
cegma
N/A
Diamond 0.8.31 module load diamond
diamond
 module load diamond/0.9.9
ELPH 1.0.1 elph N/A
EMBOSS /opt/bio/EMBOSS/bin/* module load emboss/6.6.0
EvidenceModeler 1.1.1  module load EvidenceModeler module load EVidenceModeler
Exonerate 2.4.0 module load exonerate
exonerate
FASTA Program Package 36 /opt/bio/fasta/* N/A
GenomeTools 1.5.1 gt N/A
Get_Homologues 20160802 module load get_homologues/20160802 N/A
gffutils Python package 0.8.7.1 import gffutils
GLIMMER
3.02 g3-iterated.csh:
g3-from-training.csh:
g3-from-scratch.csh
N/A
HMMER 3.1b2 module load hmmer module load hmmer
InterPro 5.21-60.0 module load InterProScan/5.21-60.0 module load interproscan/5.21-64.0
MAKER  2.31.9 module load maker module load maker
maker
MEME suite 4.11.2_2 module load meme module load meme
NCBI BLAST Suite 2.4.0 module load blast/2.3.o

blastall:blastn:blastp:
blastx:tblastn:tblastx

module load blast/2.4.o
blastall:blastn:blastp:
blastx:tblastn:tblastxBlast legacy package:
module load blast/2.2.25
blastall:blastn:blastp:
blastx:tblastn:tblastx
PASA 20140417 Launch_PASA_pipline.pl N/A
Prokka 1.11 module load prokka module load prokka
prokka
PRODIGAL 2.60 prodigal N/A
RAPSearch2 rapsearch N/A
ShortStack ShortStack N/A
SNAP 2013-11-29 snap module load snap
snap
USEARCH 9.0.2132 usearch module load usearch
usearch
VSEARCH 1.1.1 vsearch N/A

Chip-Seq Analysis

MACS2 2.1.1.20160309 module load macs2 module load macs2
macs2
QuEST 2.3 python
/opt/bioinformatics/quast-2.3/quast.py
module load quast/4.2

quast.py

Genome Assembly

ABySS2 2.0.2 kmer=64;
2.0.2-96 kmer=96
ABYSS module load abyss/2.0.2
AlignGraph 1.0 AlignGraph module load AlignGraph/v1
AlignGraph
ALLPATHS-LG 44849 RunAllPathsLG N/A
Canu 1.4 module load canu/1.5 module load canu/1.4
Celera Assembler 8.1 runCA N/A
DISCOVAR de novo module load DiscovarDeNovo/52488

NUM_THREADS=n

 module load DiscovarDeNovo/52488
Jellyfish 2.2.6 module load jellyfish
MaSURCA 3.2.2 module load MaSuRCA/3.2.1 module loadMaSuRCA/3.2.2
MeGAMerge 1.1 module load megamerge
MEGAHIT 1.1.2 N/A module load megahit/1.1.2
NxTrim 0.4.1 module load NxTrim/0.4.1  module load NxTrim/0.4.1
Phred/Phrap 1.090518 phred:phrap module load phrap/1.090518
Platanus 1.2.4 module load Platanus/1.2.4  module load Platanus/1.2.4
QUAST 2.3/4.2 python
/opt/bioinformatics/quast-2.3/quast.py
module load quast
sga 0.10.13 sga N/A
SOAP-denovo 2.04 SOAPdenovo-63mer module load SOAP-denovo/2.04

SOAPdenovo-63mer

SOAPdenovo-127mer

SPAdes 3.10.0 module load SPAdes/3.10.0 module load SPAdes/3.11.1
SSPACE(BASIC) 2.0 perl /opt/bioinformatics
/SSPACE-BASIC-2.0_linux-x86_64/
SSPACE_Basic_v2.0.pl
N/A
SSPACE(LongRead) 1-1 perl /opt/bioinformatics/SSPACE-
LongRead/SSPACE-LongRead.pl
N/A
SSPACE(STANDARD) 3.0 perl /opt/bioinformatics/SSPACE-STANDARD/SSPACE_Standard_v3.0.pl (module load SSPACE/3.0)
Supernova 1.1.4 module load Supernova/1.1.4 (highmem.q only) N/A
Velvet 1.2.10 velveth:velvetg module load velvet/1.2.10

velveth : velvetg

BBMAP 34.x module load BBMap

bbmap.sh

module load bbmap/37.41

bbmap.sh

Metagenomics

crAss 0.3.6 crass N/A
Emperor 0.9.3 make_emperor.py N/A
Genovo 0.4 assemble:finalize:compute_score_denovo N/A
HUMAnN2 v0.11.0  module load humann2  N/A
Kraken 0.10.5 module load Kraken/0.10.5

It will also define the environmental variables
$KRAKEN_DB_PATH
$KRAKEN_DEFAULT_DB

module load kraken/1.0

standard db path = /isg/shared/databases/kraken/standard

MetaBAT 2.12.1 N/A module load metabat/2.12.1
MetaVelvet 1.2.02 meta-velvetg module load MetaVelvet

meta-velvetg

Mothur 1.39.5 module load Mothur/1.39.5 module load mothur/1.39.5
Omega 1.0.2 omega N/A
Qiime 1.9.1 module load qiime module load qiime
Ray 2.3.1 module load Ray/Ray-2.3.1  Ray N/A
SPHINX 1.2b2 sphinx-sild N/A

RNA Structure

Gromacs  2016.1 module load Gromacs module load Gromacs
REAPR 1.0.18 module load reapr module load reapr
RNAsalsa 0.8.1 RNAsalsa N/A

Sequence Alignment

Clustal-Omega 1.1.0 clustalo N/A
ClustalW 2.1 clustalw2 N/A
Infernal 1.1.1 cmbuild:cmcalibrate:
cmsearch:cmscan:cmalign
module load infernal

cmbuild:cmcalibrate:cmsearch

cmscan:cmalign:cmemit

KaKsCalculator 2.0 module load KaKsCalculator/2.0

KaKsCalculator

N/A
MAFFT 7.305 module load mafft module load mafft
MUMMER 3.23 mummer module load MUMmer/3.23
Muscle 3.8.31 muscle module load muscle/3.8.31
PyNAST 1.2.2 pynast N/A
SeqTools 4.42.1 module load seqtools/4.42.1 N/A
T-Coffee 8.99 t_coffee N/A
TrimAI 1.4 module load trimal
trimal
N/A

Phylogenetics

BayesPhylogenies 2.0 /common/bayesphy/BayesPhy N/A
BayesTraits

BayesTraits_OpenMP

BayesTraits_OpenMP_Quad

2.0

2.0

2.0

module load BayesTraits/2.0
BayesTraits TreeFile
DataFileMP = multi-threaded;
Quad = quadruple precision
N/A
BEST 2.3 best N/A
CONSEL .1.2 consel N/A
CheckM 1.0.7 N/A module load CheckM/1.0.7
DiscoMark 0.9 module load discomark
cd discomark
python run_project.py
N/A
FastTree 2.1.3 FastTree N/A
GARLI 2.0 Garli-2.0 N/A
HyPhy 2.11b HYPHYMP N/A
IQ-TREE  1.5.5 N/A module load iqtree/1.5.5
Jmodeltest 2.1.4  java -jar /opt/bioinformatics/jmodeltest-2.1.4/jModelTest.jar

(need to have the X11 running)

N/A
Mauve Nov 11 2009 module load Mauve
progressiveMauve:mauveAligner
N/A
Migrate-N 4.2.14 module load migrate-n/4.2.14
migrate-n
module load migrate/3.6.11

migrate-n

migrate-n-mpi

Migrate-N-MPI 4.2.14 #$ -S /bin/bash
#$ -cwd
#$ -pe orte 7
module load migrate-n/4.2.14
mpirun -np 7 migrate-n-mpi myparmfile
N/A
MrBayes 3.2.6 module load mrbayes/3.2.6
mb
N/A
nhPhyB nhpb N/A
OrthoFinder 1.1.4 module load OrthoFinder/1.1.4 module load OrthoFinder/1.1.8
PAML 4.6 evolver:basemlg:mcmctree:pamp:yn00:chi2 N/A
PAUP 4.0a157 module load paup/current
paup
N/A
PHLAWD 3.3a phlawd N/A
Phycas 1.2.0 N/A
PhyloBayes 4.1c module load phylobayes/4.1c
pb
N/A
PhyML 3.0 PhyML_3.0_linux64 N/A
PHYLIP N/A
ProtTest 3.3 cd /opt/bioinformatics/
prottest-3.3java -jar prottest-3.3.jar
N/A
poy4 4.1.3 poy4 N/A
P4 2.0 p4 N/A
RAxML 8.3.17 raxmlHPC module load RAxML/8.2.11

raxmlHPC

Seq-Gen 1.3.3 seq-gen N/A
TreeFinder 2011.03 treefinder N/A
Tree-Puzzle 5.2 puzzle N/A

Population Genetics

BAPS 6.0 /opt/bioinformatics2/BAPS (module load BAPS)
BayesAss 3.0.4 module load BayesAss (module load BayesAss)
fastStructure  1.0 python
/opt/bioinformatics/fastStructure/structure.py
module load fastStructure
Migrate 3.6.4 migrate-n-mpi N/A
mlRho 2.0 /opt/bioinformatics2/MlRho_2.0/mlRho N/A
qctool  1.4 N/A module load qctool/1.4
Structurama /export/apps/st2 N/A
Structure 2.3.4 structure module load structure
CodonW  1.4.4 module load codonw/1.4.4
codonw
N/A

Proteomics

MASCOT /common/mascot/bin/mascot N/A
MS-GF+ 9881 java -Xmx3500M -jar /opt/bioinformatics/MSGFPlus/MSGFPlus.jar N/A
MyriMatch 2.1 N/A
Luciphor 2013.04.03 N/A
OMSSA  2.1.8 module load omssa/2.1.9
Peptide Shaker 1.14.6 module load peptideshaker
java -jar $PEPTIDESHAKER
 module load Peptideshaker
java -jar $PEPTIDESHAKER
SearchGUI 1.15.0 java -cp /opt/bioinformatics/
SearchGUI-1.15.0/SearchGUI-X.Y.Z.jar
N/A
X!Tandem 2013.09.1 N/A

 RAD-Seq

pyRAD 3.0.6 module load pyrad
pyRAD
N/A
Rainbow 2.0.3 rainbow N/A
Stacks 1.44 module load stacks module load stacks

Repeat Identification

MREPS 2.5 mreps N/A
Palfinder 0.2.04 module load pal_finder/0.02.04  N/A
RECON 1.08 module load recon module load RECON
RepeatMasker open-4.0.6 RepeatMasker module load RepeatMasker
RepeatModeler 1.0.8 RepeatModeler module load RepeatModeler
RepeatScout 1.0.5 RepeatScout module load RepeatScout
RMBlast 2.2.28 module load rmblastn module load rmblastn
Tandem Repeats Finder 4.09 trf module load TRF
ARAGORN 1.2.38 module load aragorn module load aragorn/1.2.37
BRAKER1 1.9 module load braker
braker
module load BRAKER/1.9

RNA-Seq

eXpress 1.5.1 express module load express
Cufflinks 2.2.1 cufflinks module load cufflinkss
Edge-Pro 1.3.1 /opt/bioinformatics/EDGE_pro_v1.3.1/edge.pl module load EDGE_pro
Kallisto  0.42.4 kallisto module load kallisto/0.42.4
RNA-STAR 2.5.2a module load STAR/2.5.2a module load STAR/2.5.2a
rsem 1.3.0/1.3.1 module load RSEM/1.3.0
rsem-prepare-reference: rsem-calculate-expression: rsem-sam-validator
module load RSEM/1.3.1
rsem-prepare-reference: rsem-calculate-expression: rsem-sam-validator
StringTie  2.4.1 module load stringtie
stringtie
N/A
TopHat 2.1.1 module load tophat
tophat
CAP3 02.10.15 module load cap3 module load CAP3
CD-HIT 4.6/4.6.5 module load cd-hit module load cdhit
MCL 14-137 mcl module load mcl

Short Read Alignment and Quality Control

AmpliconNoise 1.29 /opt/AmpliconNoiseV1.29 module load AmpliconNoise/1.29
AfterQC 0.9.0 module load AfterQC/0.9.0  module load AfterQC/0.9.0
bamtools 2.4.1 module load bamtools/2.4.1
bamtools
FastQC  v0.11.5 module load fastqc
fastqc
FASTX_Toolkit 0.0.13 /share/apps/fastx* module load fastx/0.0.10
freec 9.5 module load freec/9.5 N/A
HTSeq htseq-qa:htseq-count:
python -m HTSeq.scripts.count
N/A
illumina-utils filter-merged-reads N/A
MultiQC 1.1 N/A module load MultiQC/1.1
phd2fasta phd2fasta N/A
Pysam : Python package 0.11.2.2 N/A module load pysam/0.11.2.2
Quake 0.3.5 module load quake
quake.py
N/A
samtools 1.3.1 samtools module load samtools
scythe 0.991 scythe N/A
seq_crumbs 0.1.9 sff_extract:split_matepairs:
filter_by_quality:filter_duplicates
N/A
sickle 1.33 sickle module load sickle
SolexaQA++ v3.1.3 solexaqa N/A
Trimmomatic 0.36 java -jar /opt/bioinformatics/Trimmomatic-0.36/trimmomatic-0.36jar module load Trimmomatic/0.36

java -jar $Trimmomatic

XSQ Tools 1.0 /common/XSQ_Tools/scripts/ module load XSQ_Tools
SRAToolkit 2.8.1 module load sratoolkit/2.8.1 module load sratoolkit
tbl2asn  24.1 module load tbl2asn/25.3
tbl2asn
module load tbl2asn
BFAST 0.7.0a bfast module load bfast
Bowtie 1.1.2 cd /export/apps/bowtie
bowtie
module load bowtie (version 1.0.0)
Bowtie2 2.3.1 module load bowtie2/2.3.1
BWA 0.7.15 module load bwakit module load bwa/0.7.15
GMAP 2017-03-17 module load gmap/2017-03-17
HiSAT2 2.0.5 module load hisat2/2.0.5
hisat2
R 3.3.1 module load r
R

Transcriptomics

Cell Ranger 1.2.1 module load CellRanger/1.2.1 module load CellRanger/2.0.1

idba

module load idba module load idba/1.1.3
MIRA 4.9.5 module load mira/4.9.5 module load mira/4.0.2
Oases 0.2.08 oases N/A
Trans-AbySS 1.4.8 trans-ABYSS N/A
Trinity 2.4.0 module load trinity
Trinity.pl
module load trinity/2.3.2

Trinity

bcftools 1.3.1 module load bcftools
bcftools

Variant Detection

DISCOVAR  52488 module load Discovar/52488
BOLT-LMM 

2.2

N/A module load bolt/2.2
FreeBayes

1.0.2

module load freebayes
freebayes
module load freebayes/0.9.10
GATK 3.7 module load GATK
java -jar $GATK37
module load GATK
java -jar $GATK
MuTect N/A
Long Ranger 2.1.2 module load LongRanger/2.1.2 N/A
PLINK 1.90.beta.4.4 N/A module load plink/1.90.beta.4.4
SnpEff 4.3 module load snpEff/4.3i

java -jar $SNPEFF

 module load snpEff/4.3q

java -jar $SNPEFF

VarScan 2.4.3 module load VarScan
java -jar $VARSCAN
 module load varscan/2.4.3

java -jar $VARSCAN

vcflib module load vcflib
vcftools 0.1.14 module load vcftools/0.1.14 module load vcftools/0.1.14
wise 2.2.0 genewise:genewisedb:estwise:estwisedb N/A
AutoDock Vina 1.1.2 vina N/A
consed 29 module load consed  module load consed/29.0