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Software | Version | Module | Notes |
---|---|---|---|
ANGSD | 0.931 | bioinformatics/angsd/0.931 | installed with conda |
assembly-stats | 0.1.3 | bioinformatics/assembly-stats/0_1_3 | installed with conda |
Augustus | 3.3.2 | bioinformatics/augustus/3.3.2 | installed with conda |
bbmap | 38.67 | bioinformatics/bbmap/38.67 | installed with conda; environment 'bbmap_38.67' |
bcftools | 1.9 | bioinformatics/bcftools/1.9 | gcc 7.3.0 |
Beagle | 3.2 | bioinformatics/beagle/3.2 | gcc 7.3.0 |
Beast | 1.10.4 2.6.1 | bioinformatics/beast/1.10.4 bioinformatics/beast/2.6.0 | installed with conda installed with conda |
bedtools | 2.28.0 | bioinformatics/bedtools/2.28.0 | installed with conda |
bioperl | 1.7.2 | bioinformatics/bioperl/1.7.2 | installed with conda; environment 'bioperl_1.7.2' |
biopython | 1.74 1.74_python2.7 | bioinformatics/biopython/1.74 bioinformatics/biopython/1.74_python2.7 | installed with conda; environment 'biopython_1.74' installed with conda; environment 'biopython_1.74_python2.7' |
blasr | 5.3.3 5.0 | bioinformatics/blasr/5.3.3 bioinformatics/blasr/5.0 | installed with conda transferred from Hydra-4 |
BLAST | 2.6.0 2.9.0 2.8.1 | bioinformatics/blast/2.6.0 bioinformatics/blast/2.9.0 bioinformatics/blast/2.8.1 | gcc 7.3.0 gcc 7.3.0 gcc 7.3.0 |
Blast2GO | 1.4.4 | bioinformatics/blast2go/1.4.4 | See this wiki page for more information on running |
blat | 36 | bioinformatics/blat/36 | installed with conda |
BlobTools | 1.0.1 | bioinformatics/blobtools/1.0.1 | installed with conda; environment 'blobtools_1.0.1' |
Bowtie2 | 2.3.5 | bioinformatics/bowtie2/2.3.5 | installed with conda |
BUSCO | 3.0.2 4.0.2 | bioinformatics/busco/3.0.2 bioinformatics/busco/4.0.2 | installed with conda; environment 'busco_3.0.2' installed with conda; environment '4.0.2' |
BWA | 0.7.17 | bioinformatics/bwa/0.7.17 | gcc 7.3.0 |
cactus | 2019.03.01 | bioinformatics/cactus/2019.03.01 | installed with conda; environment 'cactus_2019.03.01' |
canu | 1.8 | bioinformatics/canu/1.8 | gcc 7.3.0 |
CD-hit | 4.8.1 | bioinformatics/cd-hit/4.8.1 | |
Cutadapt | 2.4 | bioinformatics/cutadapt/2.4 | installed with conda |
FastQC | 0.11.8 | bioinformatics/fastqc/0.11.8 | java 1.8 |
gatb-minia-pipeline | 1.0 | bioinformatics/gatb-minia-pipeline | installed partly with conda; environment 'gatb-minia-pipeline' |
GATK | 3.8.1.0 4.1.3.0 | bioinformatics/gatk/3.8.1.0 bioinformatics/gatk/4.1.3.0 | java 1.8 java 1.8 |
Gblocks | 0.91b | bioinformatics/gblocks/0.91b | bioperl added to module |
GetOrganelle | 1.6.2d | bioinformatics/getorganelle/1.6.2d | installed with conda |
hmmer | 3.2.1 | bioinformatics/hmmer/3.2.1 | gcc 7.3.0 |
htslib | 1.9 | bioinformatics/htslib/1.9 | gcc 7.3.0 |
HybPiper | 1.3.1 | bioinformatics/hybpiper/1.3.1 | dependencies installed with conda; environment 'hybpiper' |
HyPhy | 2.5.1 | bioinformatics/hyphy/2.5.1 | installed with conda; environment 'hyphy_2.5.1' |
IMPUTE2 | 2.3.2 | bioinformatics/shapeit/2.r837 | installed with conda; environment 'shapeit_2.r837' |
ipyrad | 0.7.30 0.9.12 | bioinformatics/ipyrad/0.7.30 bioinformatics/ipyrad/0.9 | installed with conda; environment 'ipyrad_0.7.30' installed with conda; environment 'ipyrad_0.9' |
IQ-TREE | 1.6.12 | bioinformatics/iqtree/1.6.12 | threaded (precompiled) MPI (openmpi 7.3) and hybrid (openmpi 7.3 + openmp threads) |
JBrowse | 1.16.6 | bioinformatics/jbrowse/1.16.6 | installed with conda; environment 'jbrowse_1.16.6' |
jellyfish | 2.3.0 | bioinformatics/jellyfish/2.3.0 | gcc 7.3.0 |
julia | 1.2.0 | bioinformatics/julia/1.2.0 | gcc 7.3.0 |
MAFFT | 7.407 | bioinformatics/mafft/7.407 | installed with conda |
MAKER | 2.31.10 | bioinformatics/maker/2.31.10 | installed with conda; environment 'maker' |
MaSuRCA | 3.3.3 | bioinformatics/masurca/3.3.3 | gcc 7.3.0 |
MetaMaps | 0.1 (e23f8a8) | bioinformatics/metamaps/e23f8a8 | installed with conda and gcc 7.3.0 |
MrBayes | 3.2.7a | bioinformatics/mrbayes/3.2.7a | gcc 7.3.0, openmpi 7.3 |
migrate | 3.7.2 4.4.4 3.6.11 | bioinformatics/migrate/3.7.2 bioinformatics/migrate/4.4.4 bioinformatics/migrate/3.6.11 | gcc 7.3.0, mpich 7.3 gcc 7.3.0, mpich 7.3 gcc 4.9.2 (no MPI version) |
oma | 2.3.1 | bioinformatics/oma/2.3.1 | |
Orthofinder | 2.2.7 | bioinformatics/orthofinder/2.2.7 | installed with conda; environment 'orthofinder_2.2.7' |
OrthoMCL | 2.0.9 | bioinformatics/orthomcl/2.0.9 | installed with conda; environment 'orthomcl_2.0.9' |
PAML | 4.9 4.9j | bioinformatics/paml/4.9 bioinformatics/paml/4.9j | installed with conda; environment 'paml_4.9' gcc 7.3.0 |
Partitionfinder | 2.1.1 | bioinformatics/partitionfinder/2.1.1 | added python 2.7 to module |
Phylobayes | 4.1c | bioinformatics/phylobayes/4.1c | installed with conda; environment 'phylobayes_4.1c' |
Phyluce | 1.6.7 1.5_tg | bioinformatics/phyluce/1.6.7 bioinformatics/phyluce/1.5_tg | installed with conda; environment 'phyluce_1.6.7' transferred from Hydra-4 |
Picard-tools | 2.20.6 | bioinformatics/picard-tools/2.20.6 | java 1.8 |
Pilon | 1.23 | bioinformatics/pilon/1.23 | java 1.8 |
PLINK | 1.90b4 | bioinformatics/plink/1.90b4 | installed with conda |
Proteinortho | 6.0.6 | bioinformatics/proteinortho/6.0.6 | installed with conda; environment 'proteinortho_6.0.6' |
PSMC | 0.6.5 | bioinformatics/psmc/0.6.5 | gcc 7.3.0 |
Python | 2.7 3.7 | tools/python/2.7 tools/python/3.7 | installed with anaconda; also includes mpi4py installed with anaconda; also includes mpi4py |
QIIME2 | 2019.7 | bioinformatics/qiime2/2019.7 | installed with conda; environment 'qiime2-2019.7' |
R | 3.6.1 | bioinformatics/R/3.6.1 | gcc 7.3.0, java 1.8 |
RAxML | 8.2.12 8.2.12-mpi ng-0.9.0 | bioinformatics/raxml/8.2.12 bioinformatics/raxml/8.2.12-mpi bioinformatics/raxml/ng-0.9.0 | gcc 7.3.0 openmpi 7.3 precompiled |
RepeatMasker | 4.0.9 | bioinformatics/repeatmasker/4.0.9 | |
RepeatModeler | 1.0.11 | bioinformatics/repeatmodeler/1.0.11 | installed with conda; environment 'repeatmodeler' |
revbayes | 1.0.11 | bioinformatics/revbayes/1.0.11 | gcc 4.9.2, cmake 3.31 |
Ruby | 2.6.3 | bioinformatics/ruby/2.6.3 | gcc 7.3.0 |
salmon | 0.14.1 | bioinformatics/salmon/0.14.1 | installed with conda; environment 'salmon_0.14.1' |
SHAPEIT | 2.r837 | bioinformatics/shapeit/2.r837 | installed with conda; environment 'shapeit_2.r837' |
smc++ | 1.15.2 | bioinformatics/smc++/1.15.2 | installed with conda; environment 'smc++_1.15.2' |
spades | 3.11.1 3.12.0 3.14.0 | bioinformatics/spades/3.11.1 bioinformatics/spades/3.12.0 bioinformatics/spades/3.14.0 | precompiled precompiled precompiled |
Stacks | 1.48 2.4.1 | bioinformatics/stacks/1.48 bioinformatics/stacks/2.4.1 | gcc 7.3.0 gcc 7.3.0 |
Structure | 2.3.4 | bioinformatics/structure/2.3.4 | |
Supernova | 2.1.1 | bioinformatics/supernova/2.1.1 | precompiled |
Transdecoder | 5.5.0 | bioinformatics/transdecoder/5.5.0 | bioperl, BLAST added to module |
TrimGalore! | 0.6.4 | bioinformatics/trim_galore/0.6.4 | FastQC, Cutadapt added to module |
Trimmomatic | 0.39 | bioinformatics/trimmomatic/0.39 | java 1.8 |
Trinity | 2.8.5 r2013_2_25 | bioinformatics/trinity/2.8.5 bioinformatics/trinity/r2013_2_25 | installed with conda; environment 'trinity_2.8.5' transferred from Hydra-4 |
Trinotate | 3.2.0 | bioinformatics/trinotate/3.2.0 | bioperl added to module |
vcflib | 1.0.0-rc3 | bioinformatics/vcflib/1.0.0-rc3 | gcc 7.3.0 |
vcftools | 0.1.16 | bioinformatics/vcftools/0.1.16 | gcc 7.3.0 |
Velvet | 1.2.10 | bioinformatics/velvet/1.2.10 | installed with conda; environment 'velvet_1.2.10' |
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