Software

More than 200 bioinformatics packages are installed and available on Zorbas, covering several analyses. Some of them are listed in the following categories: 

Software packageversionPATH“Big”
aragorn1.2.36
Software package version PATH “Big”
abyss 1.5.2, 2.0.2
amos 3.1.0
busco 2.0, 3.0.2b, 3.1.0
canu 1.3, 1.6, 1.8
CEGMA 2.5
cuffmerge 1.0.0
Flye 2.4.2, 2.5
Jellyfish global 1, 2.1.4, 2.3.0
K-Mer Counter (KMC) 3.1.1
MaSuRCA 3.2.3, 3.2.4, 3.2.5, 3.2.9, 3.3.0
MECAT2 v2
Mira 3.4.1.1, 4.0.2
nanopolish 0.11.1
NaS v1
oases 0.2.08
pilon 1.23.0
quast 4.4, 4.5.0, 5.0.2
Ray 2.3.1
Reapr 1.0.18
SPAdes 3.11.1, 3.13.0
ssake 3.8.0, 3.8.2
transabyss 1.5.2
TrinityRNASeq 2.1.1, 2.2.0, 2.8.4, 2.8.5
TULIP 0.4
Velvet 1.2.10
Software package version PATH “Big”
cafe 4.0.2
Software packageversionPATH“Big”
bwa0.7.15-r1140, 0.7.15, 0.7.4
Software packageversionPATH“Big”
esom1.1
AmpliconNoise1.29
anvio5.3
app-deploy-qiime1.5.0
biom-format0.9.3
CONCOCT1.1.0
ecopcr0.1
ecoPrimers0.3, 1.0
idba1.1.0
Kaiju1.7.2
Kraken1.0.0, 2.0.7
MaxBin2.2.6
metAMOS1.5rc3
Mothur1.36.1, 1.38.1, 1.42.1
OBITools1.1.16, 1.1.22, 1.2.0
Qiime1.4.0, 1.5.0, 1.8.0
Software package version PATH “Big”
AdapterRemoval 1.5.2
bam2fastq 1.1.0
bedtools 2.17.0, 2.22.1
bowtie 1.0.0, 1.2.2, 2.1.0, 2.3.5.1
BRANCH 1.8.1
CASHX 2.3
CPC2 0.1, 0.9-r2
cutadapt 1.7dev, 1.12, 2.5
deconseq 0.4.3
dwgsim 1.1.2-537
ea-utils 1.1.2-537
fastp 0.20.0
FastQC 0.11.1, 0.11.5, 0.11.8
fastx_toolkit 0.0.13, 0.0.13.2, 0.0.14, 0.0.6
FLASH 1.2.6
gatb-core 1.0.4
GENE-counter 0.4.4
LoRDEC 0.3, 0.6
minimap 0.2-r123, 2.17-r954-dirty
Mummer 4.0.0beta2
nanopolish 0.11.1
NGSQCToolkit 2.3.3
ngutils 0.5.0c
oases 0.2.08
picard-tools 1.140, 1.68, 1.91, 2.19.1
pIRS 1.10
prinseq-lite 0.20.3
Ray 2.1.0
ribopicker 0.4.3
rsem 1.2.17
samtools 0.1.19, 1.2, 1.3.1, 1.5, 1.9
scythe 0.991
seqtk 1.0-r64-dirty
sickle 1.33
sra toolkit 2.2.2a, 2.3.2-4
ssake 3.8.0, 3.8.2
STAR 2.4.0b
tabix 0.2.6
tagcleaner 0.16
tophat 2.0.12
Trimmomatic 0.30, 0.32, 0.39
TrinityRNASeq 2.1.1, 2.2.0, 2.8.4, 2.8.5
Software package version PATH “Big”
DALIGNER 20141231
DAMe 1.0
fastx_toolkit 0.0.13, 0.0.13.2, 0.0.14, 0.0.6
LoRDEC 0.3, 0.6
pandaseq 2.11
pear 0.9.6
Porechop Oct 2018
proovread 2.13.11
Software packageversionPATH“Big”
Crimap2.507
Pyrad2.16.1, 3.0.5
Stacks

1.47, 2.0, 2.2, 2.3e, 2.4/td>

Software package version PATH “Big”
OMA 2.1.1
Software package version PATH “Big”
beast 2.4.2
exabayes 1.4.1
fasttree 2.1.9, 2.1.10
garli 2.01
hamstr 13.2.2, 13.2.6
jModelTest 2.1.4
MrBayes 3.1.2h, 3.2.6, 3.2.7a, 3.2.7a-MPI
phylobayes (MPI) 3.3f, 4.1c
phyml (MPI) 20120412, 3.3.20190321
pplacer 1.1
PRANK v.140603
RAxML 8.0.23, 8.2.9
Software package version PATH “Big”
dDocent 2.12
Genepop 4.5.1
Software package version PATH “Big”
PLINK v1.90b4.4
Software package version PATH “Big”
augustus 3.2.3
bcftools 1.9
bedtools 2.17.0, 2.22.1
BRAKER 1.9
busco 2.0, 3.0.2b, 3.1.0
cd-hit 0.5-2012-03-07, cluster-consensus-2013-03-27, 4.5.8, 4.6, 4.6.1
circos 0.69-4, 0.69-5
clinEff 1.0h
CPAT 1.0.0
CPC2 0.1, 0.9-r2
EMBOSS 6.2.0, 6.3.1, 6.6.0.0
ESTscan 3.0.3
fastx_toolkit 0.0.13, 0.0.13.2, 0.0.14, 0.0.6
FreeBayes v1.2.0-4-gd15209e
gffCompare 0.9.5
Glimmer 3.02
hmmer 3.1b1, 3.1b2
Kalign 2.04
LeMoNe 2.5
Maker 2.31.10
Marxan 2.43
microbiomeutil r20110519
migrate 3.3.2
modules 3.2.10
MrBayes 3.1.2h, 3.2.6, 3.2.7a, 3.2.7a-MPI
ncbi-blast 2.6.0
OBITools 1.1.16, 1.1.22, 1.2.0
orthomclSoftware 2.0.9
phobos 3.3.12
PhredPhrap v1.090518
phyml (MPI) 20120412, 3.3.20190321
picard-tools 1.140, 1.68, 1.91, 2.19.1
quast 4.4, 4.5.0, 5.0.2
rdp classifier 2.12
salmon 0.14.1
samstat 1.5.1
samtools 0.1.19, 1.2, 1.3.1, 1.5, 1.9
singularity 2.3.1, 3.3.0-1
snpEff 4.3t
sra toolkit 2.2.2a, 2.3.2-4
tacg 4.1.0
TransDecoder 2.1.0
vcflib v1.0.0-rc0-333-g5b0f
ViennaRNA 2.4.12
vsearch 0.0.4 – 1.1.3, 2.4.12
xoreos-tools 0.0.5

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