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The StaPH-B/docker-builds repository is licensed under GNU GPLv3 as of 2020-01-16 (commit: https://github.com/StaPH-B/docker-builds/commit/a4f6e3c7cd7f82aab5117f6f48a292a48cc1091a )

In this repository you will find numerous dockerfiles, but no source code of the programs we have built docker images for. The one exception to this is Serotypefinder, which is licensed under Apache 2.0, and allows for the re-distribution of the source code.

The licenses of the open-source software that is contained in these Docker images should be listed in each dockerfile's metadata, but is also listed in the table below.

Software License Link to license
ABRicate GNU GPLv2 https://github.com/tseemann/abricate/blob/master/LICENSE
ACI MIT https://github.com/erinyoung/ACI/blob/main/LICENSE
ANIclustermap MIT https://github.com/moshi4/ANIclustermap/blob/main/LICENSE
artic MIT https://github.com/artic-network/fieldbioinformatics/blob/master/LICENSE
artic-ncov2019-epi2me MPL 2.0 https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE
any2fasta GNU GPLv3 https://github.com/tseemann/any2fasta/blob/master/LICENSE
ARIBA GNU GPLv3 https://github.com/sanger-pathogens/ariba/blob/master/LICENSE
assembly_snptyper MIT https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE
Augur GNU Affero GPLv3 https://github.com/nextstrain/augur/blob/master/LICENSE.txt
Auspice GNU Affero GPLv3 https://github.com/nextstrain/auspice/blob/master/LICENSE.txt
Bakta GNU GPLv3 https://github.com/oschwengers/bakta/blob/main/LICENSE
Bandage GNU GPLv3 https://github.com/rrwick/Bandage?tab=GPL-3.0-1-ov-file#readme
BBTools non-standard - see licence.txt and legal.txt that is included in docker image under /bbmap/docs/; Also on sourceforge repo for BBTools https://jgi.doe.gov/disclaimer/
bcftools MIT & GNU GPLv3 https://github.com/samtools/bcftools/blob/develop/LICENSE
bedtools MIT https://github.com/arq5x/bedtools2/blob/master/LICENSE
blast+ Public Domain https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE
bowtie2 GNU GPLv3 https://github.com/BenLangmead/bowtie2/blob/master/LICENSE
Bracken GNU GPLv3 https://github.com/jenniferlu717/Bracken/blob/master/LICENSE
BUSCO MIT https://gitlab.com/ezlab/busco/-/raw/master/LICENSE
BWA GNU GPLv3 https://github.com/lh3/bwa/blob/master/COPYING
Canu
Racon
Minimap2		 GNU GPLv3 (Canu),
MIT (Racon),
MIT (Minimap2)		 https://github.com/marbl/canu/blob/master/README.license.GPL https://github.com/isovic/racon/blob/master/LICENSE https://github.com/lh3/minimap2/blob/master/LICENSE.txt
CAT MIT https://github.com/MGXlab/CAT_pack?tab=MIT-1-ov-file#readme
centroid GitHub No License https://github.com/https://github.com/stjacqrm/centroid
CDC-SPN GitHub No License https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline non-standard license see --> https://github.com/CFSAN-Biostatistics/snp-pipeline/blob/master/LICENSE.txt
CheckM GNU GPLv3 https://github.com/Ecogenomics/CheckM/blob/master/LICENSE
CheckM2 GNU GPLv3 https://github.com/chklovski/CheckM2/blob/main/LICENSE
CheckV MIT https://bitbucket.org/berkeleylab/checkv/src/master/LICENSE.txt
Circlator GNU GPLv3 https://github.com/sanger-pathogens/circlator/blob/master/LICENSE
Circos GNU GPLv3 https://circos.ca/
CirculoCov GNU GPLv3 https://github.com/erinyoung/CirculoCov/blob/main/LICENSE
Clair3 non-standard https://github.com/HKU-BAL/Clair3/blob/main/LICENSE.md
colorid MIT https://github.com/hcdenbakker/colorid/blob/master/LICENSE
Core-SNP-filter GNU General Public License v3.0 https://github.com/rrwick/Core-SNP-filter/blob/main/LICENSE
datasets-sars-cov-2 Apache 2.0 https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE
diamond GNU GPLv3 https://github.com/bbuchfink/diamond/blob/master/LICENSE
dnaapler MIT https://github.com/gbouras13/dnaapler/blob/main/LICENSE
dorado Oxford Nanopore Technologies PLC Public License ONT License
dragonflye GNU GPLv3 https://github.com/rpetit3/dragonflye/blob/main/LICENSE
drprg MIT https://github.com/mbhall88/drprg/blob/main/LICENSE
DSK GNU Affero GPLv3 https://github.com/GATB/dsk/blob/master/LICENSE
el_gato MIT https://github.com/appliedbinf/el_gato/blob/main/LICENSE
emboss GNU GPLv3 http://emboss.sourceforge.net/licence/
emmtyper GNU GPLv3 https://github.com/MDU-PHL/emmtyper/blob/master/LICENSE
emm-typing-tool GNU GPLv3 https://github.com/phe-bioinformatics/emm-typing-tool/blob/master/LICENCE
EToKi GNU GPLv3 https://github.com/zheminzhou/EToKi/blob/master/LICENSE
FastANI Apache v2.0 https://github.com/ParBLiSS/FastANI/blob/master/LICENSE
fasten MIT https://github.com/lskatz/fasten/blob/master/LICENSE
Fastp MIT https://github.com/OpenGene/fastp/blob/master/LICENSE
FastTree GNU GPLv2 http://www.microbesonline.org/fasttree/
FastQC GNU GPLv3 https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt
fastq-scan MIT https://github.com/rpetit3/fastq-scan/blob/master/LICENSE
Freebayes MIT https://github.com/freebayes/freebayes/blob/master/LICENSE
Filtlong GNU GPLv3 https://github.com/rrwick/Filtlong/blob/master/LICENSE
FLASH GNU GPLv3 https://github.com/ebiggers/flash/blob/master/COPYING
Flye BSD-3 https://github.com/fenderglass/Flye/blob/flye/LICENSE
Freyja BSD-2 https://github.com/andersen-lab/Freyja/blob/main/LICENSE
GAMBIT GNU aGPLv3 https://github.com/jlumpe/gambit/blob/master/LICENSE
GAMMA Apache 2.0 https://github.com/rastanton/GAMMA/blob/main/LICENSE
GenoFlu GNU GPL v3 https://github.com/USDA-VS/GenoFLU/blob/main/LICENSE
Genotyphi GNU GPLv3 https://github.com/katholt/genotyphi/blob/main/LICENSE
geNomad ACADEMIC, INTERNAL, RESEARCH & DEVELOPMENT, NON-COMMERCIAL USE ONLY https://github.com/apcamargo/genomad/blob/main/LICENSE
GenoVi BY-NC-SA Creative Commons License https://github.com/robotoD/GenoVi/blob/main/LICENSE.txt
gfastats MIT https://github.com/vgl-hub/gfastats/blob/main/LICENSE
Grandeur GNU General Public License v3.0 https://github.com/UPHL-BioNGS/Grandeur/blob/main/LICENSE
Gubbins GNU GPLv2 https://github.com/nickjcroucher/gubbins/blob/master/LICENSE
HeatCluster GPL-3.0 https://github.com/DrB-S/heatcluster/blob/main/LICENSE
Hmmer BSD-3 http://eddylab.org/software/hmmer/Userguide.pdf
homopolish GNU GPLv3 https://github.com/ythuang0522/homopolish/blob/master/LICENSE
hostile MIT https://github.com/bede/hostile?tab=MIT-1-ov-file#readme
htslib MIT https://github.com/samtools/htslib/blob/develop/LICENSE
IGV-Reports MIT https://github.com/igvteam/igv-reports/blob/master/LICENSE.md
Integron Finder GNU GPLv3 https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING
iqtree GNU GPLv2 https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE
iqtree2 GNU GPLv2 https://github.com/iqtree/iqtree2/blob/master/LICENSE
IPA BSD-3 https://github.com/PacificBiosciences/pbipa/blob/master/LICENSE.txt
IRMA GNU GPLv3 https://wonder.cdc.gov/amd/flu/irma/disclaimer.html
isPcr non-standard - see README in source https://hgwdev.gi.ucsc.edu/~kent/src/isPcr33.zip
iVar GNU GPLv3 https://github.com/andersen-lab/ivar/blob/master/LICENSE
Jasmine BSD-3 https://github.com/PacificBiosciences/jasmine/blob/main/LICENSE
Kaptive GNU GPLv3 https://github.com/katholt/Kaptive/blob/master/LICENSE
Kleborate GNU GPLv3 https://github.com/katholt/Kleborate/blob/master/LICENSE
kma Apache v2.0 https://bitbucket.org/genomicepidemiology/kma/src/master/
Kraken GNU GPLv3 https://github.com/DerrickWood/kraken/blob/master/LICENSE
Kraken2 MIT https://github.com/DerrickWood/kraken2/blob/master/LICENSE
KrakenTools GNU GPLv3 https://github.com/jenniferlu717/KrakenTools/blob/master/LICENSE
KrakenUniq GNU GPLv3 https://github.com/fbreitwieser/krakenuniq/blob/master/LICENSE
kSNP3 BSD available in zipped kSNP archive on sourceforge or in docker image under /kSNP3.1_Linux_package/THE BSD OPENSOURCE LICENSE.pdf
kSNP4 BSD available in zipped kSNP archive on sourceforge or in docker image under /opt/kSNP4 Linux package/Documentation/THE BSD OPENSOURCE LICENSE.pdf
LABEL GPL version 3 In zipped file in README.md
legsta GNU GPLv3 https://github.com/tseemann/legsta/blob/master/LICENSE
liftoff GNU GPLv3 https://github.com/agshumate/Liftoff/blob/master/LICENSE.md
lima BSD-3 https://github.com/PacificBiosciences/barcoding/blob/master/LICENSE
longshot MIT https://github.com/pjedge/longshot/blob/master/LICENSE
lrge MIT https://github.com/mbhall88/lrge?tab=MIT-1-ov-file#readme
Lyve-SET MIT https://github.com/lskatz/lyve-SET/blob/master/LICENSE
Mafft BSD https://mafft.cbrc.jp/alignment/software/license.txt
Mash non-standard license (see link) https://github.com/marbl/Mash/blob/master/LICENSE.txt
mashtree GNU GPLv3 https://github.com/lskatz/mashtree/blob/master/LICENSE
MaSuRCA GNU GPLv3 https://github.com/alekseyzimin/masurca/blob/master/LICENSE.txt
Medaka Mozilla Public License 2.0 https://github.com/nanoporetech/medaka/blob/master/LICENSE.md
meningotype GNU General Public License v3.0 https://github.com/MDU-PHL/meningotype/blob/master/LICENSE
Metaphlan MIT https://github.com/biobakery/MetaPhlAn/blob/master/license.txt
MIDAS GNU GPLv3 https://github.com/snayfach/MIDAS/blob/master/LICENSE
minimap2 MIT https://github.com/lh3/minimap2/blob/master/LICENSE.txt
miniasm MIT https://github.com/lh3/miniasm/blob/master/LICENSE.txt
minipolish GNU GPLv3 https://github.com/rrwick/Minipolish/blob/main/LICENSE
mlst GNU GPLv2 https://github.com/tseemann/mlst/blob/master/LICENSE
Mugsy Artistic License 2.0 Archived in:
https://sourceforge.net/projects/mugsy/files/mugsy_x86-64-v1r2.3.tgz
MultiQC GNU GPLv3 https://github.com/ewels/MultiQC/blob/master/LICENSE
Mummer The Artistic License 2.0 https://github.com/mummer4/mummer/blob/master/LICENSE.md
Mykrobe MIT https://github.com/Mykrobe-tools/mykrobe/blob/master/LICENSE
NanoPlot GNU GPLv3 https://github.com/wdecoster/NanoPlot/blob/master/LICENSE
NCBI AMRFinderPlus Public Domain https://github.com/ncbi/amr/blob/master/LICENSE
NCBI Datasets Public Domain https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md
NCBI table2asn Public Domain unknown
ngmaster GNU GPLv3 https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE
ONTime MIT https://github.com/mbhall88/ontime/blob/main/LICENSE
OrthoFinder GNU GPLv3 https://github.com/davidemms/OrthoFinder/blob/master/License.md
Panaroo MIT https://github.com/gtonkinhill/panaroo/blob/master/LICENSE
pandas BSD 3-Clause License https://github.com/pandas-dev/pandas?tab=BSD-3-Clause-1-ov-file#readme
pango_aliasor MIT https://github.com/corneliusroemer/pango_aliasor/blob/main/LICENSE
Pangolin GNU GPLv3 https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt
panqc MIT https://github.com/maxgmarin/panqc/blob/main/LICENSE
Parsnp Battelle National Biodefense Institute (BNBI) https://github.com/marbl/parsnp?tab=License-1-ov-file#readme
pasty Apache 2.0 https://github.com/rpetit3/pasty/blob/main/LICENSE
Pavian GNU GPLv3 https://github.com/fbreitwieser/pavian/blob/master/DESCRIPTION
pbmm2 BSD-3 https://github.com/PacificBiosciences/pbmm2/blob/develop/LICENSE
pbptyper MIT https://github.com/rpetit3/pbptyper/blob/main/LICENSE
pbtk BSD-3 https://github.com/PacificBiosciences/pbtk/blob/main/LICENSE.txt
Phyml GNU GPLv3 https://github.com/stephaneguindon/phyml/blob/master/COPYING
phyTreeViz MIT https://github.com/moshi4/phyTreeViz/blob/main/LICENSE
Piggy GNU GPLv3 https://github.com/harry-thorpe/piggy/blob/master/LICENSE
Pilon GNU GPLv2 https://github.com/broadinstitute/pilon/blob/master/LICENSE
Piranha GNU GPLv3 https://github.com/polio-nanopore/piranha/blob/main/LICENSE
PlasmidSeeker BSD 3-Clause https://github.com/bioinfo-ut/PlasmidSeeker/blob/master/LICENSE
pmga GNU GPLv2 https://github.com/rpetit3/pmga/blob/master/LICENSE
polypolish GNU GPLv3 https://github.com/rrwick/Polypolish/blob/main/LICENSE
PopPUNK Apache 2.0 https://github.com/bacpop/PopPUNK/blob/master/LICENSE
Porechop GNU GPLv3 https://github.com/rrwick/Porechop/blob/master/LICENSE
PPanGGOLiN CeCILL 2.1 https://github.com/labgem/PPanGGOLiN/blob/master/LICENSE.txt
Prokka GNU GPLv3 https://raw.githubusercontent.com/tseemann/prokka/master/doc/LICENSE.Prokka
pyCirclize MIT https://github.com/moshi4/pyCirclize/blob/main/LICENSE
pyGenomeViz MIT https://github.com/moshi4/pyGenomeViz/blob/main/LICENSE
pyMLST GNU GPLv3 https://github.com/bvalot/pyMLST/blob/master/LICENSE
pypolca MIT https://github.com/gbouras13/pypolca/blob/main/LICENSE
QUAST GNU GPLv2 https://github.com/ablab/quast/blob/master/LICENSE.txt
QuickSNP GNU GPLv3 https://github.com/k-florek/QuickSNP/blob/main/LICENSE
racon MIT https://github.com/lbcb-sci/racon/blob/master/LICENSE ; https://github.com/isovic/racon/blob/master/LICENSE
rasusa MIT https://github.com/mbhall88/rasusa/blob/master/LICENSE
raven MIT https://github.com/lbcb-sci/raven/blob/master/LICENSE
RAxML GNU GPLv3 https://github.com/stamatak/standard-RAxML/blob/master/gpl-3.0.txt
RAxML-NG GNU AGPLv3 https://github.com/amkozlov/raxml-ng/blob/master/LICENSE.txt
RAxML-NG GNU GPLv2 https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html
ResFinder Apache 2.0 https://bitbucket.org/genomicepidemiology/resfinder/src/master/
Roary GNU GPLv3 https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE
SalmID MIT https://github.com/hcdenbakker/SalmID/blob/master/LICENSE
samclip GNU GPLv3 https://github.com/tseemann/samclip/blob/master/LICENSE
Samtools GNU GPLv3 https://github.com/samtools/samtools/blob/develop/LICENSE
SeqFu GNU GPLv3 https://github.com/telatin/seqfu2
SeqKit MIT https://github.com/shenwei356/seqkit/blob/master/LICENSE
SeqSero GNU GPLv2 https://github.com/denglab/SeqSero/blob/master/LICENSE
SeqSero2 GNU GPLv2 https://github.com/denglab/SeqSero2/blob/master/LICENSE
seqyclean MIT https://github.com/ibest/seqyclean/blob/master/LICENSE
seqtk MIT https://github.com/lh3/seqtk/blob/master/LICENSE
Seroba GNU GPLv3 https://github.com/sanger-pathogens/seroba/blob/master/LICENSE
SerotypeFinder Apache 2.0 https://bitbucket.org/genomicepidemiology/serotypefinder/
ShigaPass GNU GPLv3 https://github.com/imanyass/ShigaPass/blob/main/LICENSE
shigatyper non-standard license see --> https://github.com/CFSAN-Biostatistics/shigatyper/blob/master/LICENSE
ShigEiFinder GNU GPLv3 https://github.com/LanLab/ShigEiFinder/blob/main/LICENSE
Shovill GNU GPLv3 https://github.com/tseemann/shovill/blob/master/LICENSE
SISTR Apache 2.0 https://github.com/phac-nml/sistr_cmd/blob/master/LICENSE
SKA MIT https://github.com/simonrharris/SKA/blob/master/LICENSE
SKA2 Apache 2.0 https://github.com/bacpop/ska.rust/blob/master/LICENSE
skani MIT https://github.com/bluenote-1577/skani/blob/main/LICENSE
SKESA Public Domain https://github.com/ncbi/SKESA/blob/master/LICENSE
Smalt GNU GPLv3 https://www.sanger.ac.uk/tool/smalt-0/
SnpEff MIT https://github.com/pcingola/SnpEff/blob/master/LICENSE.md
Snippy GNU GPLv2 https://github.com/tseemann/snippy/blob/master/LICENSE
snp-dists GNU GPLv3 https://github.com/tseemann/snp-dists/blob/master/LICENSE
SNP-sites GNU GPLv3 https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE
SNVPhyl-tools Apache 2.0 https://github.com/phac-nml/snvphyl-tools/blob/master/LICENSE
SPAdes GNU GPLv2 https://github.com/ablab/spades/blob/spades_3.13.0/assembler/LICENSE
SRA-toolkit Public Domain https://github.com/ncbi/sra-tools/blob/master/LICENSE
SRST2 BSD https://github.com/katholt/srst2/blob/master/LICENSE.txt
Staramr Apache 2.0 https://github.com/phac-nml/staramr/blob/master/LICENSE
stxtyper Public Domain https://github.com/ncbi/stxtyper/blob/main/LICENSE
sylph MIT https://github.com/bluenote-1577/sylph/blob/main/LICENSE
TBProfiler GNU GPLv3 https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE
TipToft GNU GPLv3 https://github.com/andrewjpage/tiptoft/blob/master/LICENSE
Tostadas Apache-2.0 license https://github.com/CDCgov/tostadas/blob/master/LICENSE
toulligqc GNU GPLv3 https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt
Treemmer GNU GPLv3 https://github.com/fmenardo/Treemmer/blob/master/COPYING
Trimmomatic GNU GPLv3 https://github.com/usadellab/Trimmomatic/blob/main/distSrc/LICENSE
Trycycler GNU GPLv3 https://github.com/rrwick/Trycycler/blob/master/LICENSE
Unicycler GNU GPLv3 https://github.com/rrwick/Unicycler/blob/master/LICENSE
VADR Public Domain https://github.com/nawrockie/vadr/blob/master/LICENSE
Verkko Public Domain https://github.com/marbl/verkko/blob/master/README.licenses
VIBRANT GNU GPLv3 https://github.com/AnantharamanLab/VIBRANT/blob/master/LICENSE
VIGOR4 GNU GPLv3 https://github.com/JCVenterInstitute/VIGOR4/blob/master/LICENSE.txt
Viridian MIT https://github.com/iqbal-lab-org/viridian/blob/master/LICENSE
VirSorter2 GNU GPLv2 https://github.com/jiarong/VirSorter2/blob/master/LICENSE
VirulenceFinder Apache 2.0 https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/
wtdbg2 GNU GPLv3 https://github.com/ruanjue/wtdbg2/blob/master/LICENSE.txt