Software

Software available on the clusters are freely available for use.  Users must be comfortable in a Unix environment and understand how to properly submit jobs. Request additional information, accounts, and access here.

1. Annotation
2. Chip Seq
3. Genome Assembly
4. Metagenomics
5. Molecular Structure
6. Multiple Sequence Aligners
7. Phylogenetics
8. Population Genetics
9. Proteomics
10. RAD-Seq
11. Repeat Analysis
12. RNA-Seq
13. Sequence Clustering
14. Sequence File Manip./Quality Control
15. Sequence Submission
16. Short Read Aligners
17. Single Cell Genomics
18. Statistics
19. Transcriptome Assembly
20. Variation Detection
21. Visualization Tools

  Software Type Software Name Version Executable (case-senstitive, ‘:’ means multiple options; if module available, load it first using “module load …”)
BBC UCHC
Annotation/Sequence Search 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
CEGMA 2.5 module load CEGMA
cegma
N/A
Diamond 0.8.31 module load diamond
diamond
ELPH 1.0.1 elph N/A
EMBOSS /opt/bio/EMBOSS/bin/* N/A
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/5.21-60.0
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 2.2.29+ blastall:blastn:blastp:
blastx:tblastn:tblastx
N/A
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 MACS2 2.1.1.20160309 module load macs2 module load macs2
macs2
QuEST 2.3 python
/opt/bioinformatics/quast-2.3/quast.py
N/A
Genome Assembly ABySS2 2.0.2 kmer=64;
2.0.2-96 kmer=96
ABYSS N/A
AlignGraph 1.0 AlignGraph module load AlignGraph
AlignGraph
ALLPATHS-LG 44849 RunAllPathsLG N/A
Canu 1.4 module load canu/1.4 module load canu/1.4
Celera Assembler 8.1 runCA N/A
DISCOVAR de novo module load DiscovarDeNovo/52488

NUM_THREADS=n

Jellyfish 1.1.10 jellyfish N/A
Jellyfish 2.2.6 module load jellyfish
MaSURCA 3.2.1 module load MaSuRCA/3.2.1 module load masurca
MeGAMerge 1.1 module load megamerge
NxTrim 0.4.1 module load NxTrim/0.4.1
Phred/Phrap 1.090518 phred:phrap N/A
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
SPAdes 3.9.0 module load SPAdes
spades
SPAdes 3.10.0 module load SPAdes/3.10.0
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 N/A
Supernova 1.1.4 module load Supernova/1.1.4

(Will only run on highmem.q on BBC)

Need to assign the number of cores using:

–localcores n (n=1,2,3,4…etc)

N/A
TIGR Assembler 2.0 run_TA N/A
Velvet 1.2.10 velveth:velvetg module load velvet
Metagenomics BBMAP 34.x module load BBMap   bbmap.sh N/A
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

N/A
MetaVelvet 1.2.02 meta-velvetg module load MetaVelvet
Mothur 1.38.1 module load Mothur module load mothur
Mothur 1.39.0 module load Mothur/1.39.0 module load mothur/1.39.0
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-build N/A
Molecular 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
Multiple Sequence Aligners

Clustal-Omega 1.1.0 clustalo N/A
ClustalW 2.1 clustalw2 N/A
Infernal 1.1 cmbuild:cmcalibrate:
cmsearch:cmscan:cmalign
module load infernal
MAFFT 7.305 module load mafft module load mafft
MUMMER 3.23 mummer module load MUMmer
Muscle 3.8.31 muscle module load muscle
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
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
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
MrBayes 3.2.1 mb N/A
nhPhyB nhpb N/A
OrthoFinder 1.1.4 module load OrthoFinder/1.1.4 module load OrthoFinder/1.1.4
PAML 4.6 evolver:basemlg:mcmctree:pamp:yn00:chi2 N/A
PAUP 4.0b10 paup N/A
PHLAWD 3.3a phlawd N/A
Phycas 1.2.0 N/A
PhyloBayes 1.5a phylobayes 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 N/A
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 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
Structurama /export/apps/st2 N/A
Structure 2.3.4 structure module load structure
Proteomics CodonW  1.4.4 module load codonw/1.4.4
codonw
N/A
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 module load omssa
Peptide Shaker 1.14.6 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
ustacks:pstacks:cstacks:
sstacks:genotypes:populations
module load stacks
Repeat Analysis 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
TEClass 1.0 N/A
RNA-Seq ARAGORN 1.2.38 module load aragorn module load aragorn
BREAKER2 1.9 module load braker
braker
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 kallisto module load kallisto
RNA-STAR 2.5.2a module load STAR/2.5.2a N/A
rsem 1.3.0 module load RSEM
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
Sequence Clustering 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
Sequence File Manipulation/Quality Control AmpliconNoise 1.29 /opt/AmpliconNoiseV1.29 module load AmpliconNoise
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
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
phd2fasta phd2fasta N/A
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
XSQ Tools 1.0 /common/XSQ_Tools/scripts/ module load XSQ_Tools
Sequence Submission SRAToolkit 2.8.1 module load sratoolkit/2.8.1 module load sratoolkit
tbl2asn tbl2asn module load tbl2asn
Short Read Aligners BFAST 0.7.0a bfast module lost bfast
Bowtie 1.1.2 cd /export/apps/bowtie
bowtie
module load bowtie
Bowtie2 2.3.1 module load bowtie2/2.3.1
BWA 0.7.15 module load bwakit
GMAP 2017-03-17 module load gmap/2017-03-17
HiSAT2 2.0.5 module load hisat2/2.0.5
hisat2
Statistical Packages R 3.3.1 module load r
R
Single Cell Genomics Cell Ranger 1.2.1 module load CellRanger/1.2.1 N/A
Transcriptome Assembly

idba

module load idba
MIRA 4.9.5 module load mira
Newbler newbler N/A
Oases 0.2.08 oases N/A
Trans-AbySS 1.4.8 trans-ABYSS N/A
Trinity 2.2.0 module load trinity
Trinity.pl
Variation Detection bcftools 1.3.1 module load bcftools
bcftools
DISCOVAR module load Discovar/52488

NUM_THREADS=n

FreeBayes

1.0.2

module load freebayes
freebayes
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
SnpEff 4.3i module load snpEff/4.3i
VarScan 2.4.3 module load VarScan
java -jar $VARSCAN
vcflib module load vcflib
vcftools 0.1.13 module load vcftools/0.1.13 N/A
0.1.14 module load vcftools/0.1.14
wise 2.2.0 genewise:genewisedb:estwise:estwisedb N/A
Visualization Tool AutoDock Vina 1.1.2 vina N/A
consed 29 module load consed  module load consed