ABRicate |
- 0.8.7
- 0.8.13
- 0.8.13s (+serotypefinder db)
- 0.9.8
- 1.0.0
|
https://github.com/tseemann/abricate |
ARIBA |
|
https://github.com/sanger-pathogens/ariba |
Augur |
|
https://github.com/nextstrain/augur |
Auspice |
|
https://github.com/nextstrain/auspice |
BBTools |
|
https://jgi.doe.gov/data-and-tools/bbtools/ |
bcftools |
|
https://github.com/samtools/bcftools |
bedtools |
|
https://bedtools.readthedocs.io/en/latest/ |
BWA |
|
https://github.com/lh3/bwa |
Canu |
|
https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu |
Canu-Racon |
- 1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)
- 1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)
- 1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)
- 2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)
|
https://canu.readthedocs.io/en/latest/ https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED) https://lh3.github.io/minimap2/ |
centroid |
|
https://github.com/stjacqrm/centroid |
CDC-SPN |
|
https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
cfsan-snp-pipeline |
|
https://github.com/CFSAN-Biostatistics/snp-pipeline |
Circlator |
|
https://github.com/sanger-pathogens/circlator |
Clustalo |
|
http://www.clustal.org/omega/ |
colorid |
|
https://github.com/hcdenbakker/colorid |
cutshaw-report-env |
|
https://github.com/VADGS/CutShaw |
emm-typing-tool |
|
https://github.com/phe-bioinformatics/emm-typing-tool |
FastANI |
|
https://github.com/ParBLiSS/FastANI |
FastTree |
|
http://www.microbesonline.org/fasttree/ |
FastQC |
|
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC |
Filtlong |
|
https://github.com/rrwick/filtlong |
Flye |
|
https://github.com/fenderglass/Flye |
iqtree |
|
http://www.iqtree.org/ |
iVar |
- 1.1
- 1.1 (+SARS-CoV2 reference)
- 1.2.1
- 1.2.1 (+SC2 ref)
- 1.2.2 (+SC2 ref and artic bedfiles)
- 1.3
|
https://github.com/andersen-lab/ivar |
kma |
|
https://bitbucket.org/genomicepidemiology/kma/ |
Kraken |
- 1.0
- 1.0.0_wslh_signed
- 1.1.1
- 1.1.1 (no database)
|
https://github.com/DerrickWood/kraken |
Kraken2 |
- 2.0.8-beta (no database)
- 2.0.8-beta (MiniKraken2_v1_8GB db)
- 2.0.8-beta_hv (human + virus db)
- 2.0.9-beta (no db)
- 2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)
- 2.1.0 (no db)
- 2.1.1 (no db)
|
https://github.com/DerrickWood/kraken2 |
kSNP3 |
|
https://sourceforge.net/projects/ksnp/ |
legsta |
|
https://github.com/tseemann/legsta |
Lyve-SET (includes CG-Pipeline scripts and raxml) |
|
https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |
MAFFT |
|
https://mafft.cbrc.jp/alignment/software/ |
Mash |
|
https://github.com/marbl/Mash |
mashtree |
|
https://github.com/lskatz/mashtree |
medaka |
|
https://github.com/nanoporetech/medaka |
metaphlan |
- 3.0.3-no-db (no database)
- 3.0.3 (~3GB db)
|
https://github.com/biobakery/MetaPhlAn/tree/3.0 |
minimap2 |
|
https://github.com/lh3/minimap2 |
mlst |
|
https://github.com/tseemann/mlst |
Mugsy |
|
http://mugsy.sourceforge.net/ |
MultiQC |
|
https://github.com/ewels/MultiQC |
NanoPlot |
- 1.27.0
- 1.29.0
- 1.30.1
- 1.32.0
- 1.33.0
|
https://github.com/wdecoster/NanoPlot |
NCBI AMRFinderPlus |
- 3.1.1b
- 3.8.4
- 3.8.28
- 3.9.3
- 3.9.8
|
https://github.com/ncbi/amr |
OrthoFinder |
|
https://github.com/davidemms/OrthoFinder |
Pangolin |
- 1.1.14
- 2.0.4
- 2.0.5
- 2.1.1
- 2.1.3
- 2.1.6
- 2.1.7
|
https://github.com/hCoV-2019/pangolin |
parallel-perl |
|
https://www.gnu.org/software/parallel |
Pilon |
|
https://github.com/broadinstitute/pilon |
PlasmidSeeker |
|
https://github.com/bioinfo-ut/PlasmidSeeker |
Prokka |
|
https://github.com/tseemann/prokka |
QUAST |
|
https://github.com/ablab/quast |
racon |
|
https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED) |
rasusa |
|
https://github.com/mbhall88/rasusa |
RAxML |
- 8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation)
|
https://github.com/stamatak/standard-RAxML https://github.com/amkozlov/raxml-ng |
Roary |
|
https://github.com/sanger-pathogens/Roary |
SalmID |
|
https://github.com/hcdenbakker/SalmID |
Samtools |
|
https://github.com/samtools/samtools |
SeqSero |
|
https://github.com/denglab/SeqSero |
SeqSero2 |
- 0.1.0
- 1.0.0
- 1.0.2
- 1.1.0
- 1.1.1
|
https://github.com/denglab/SeqSero2/ |
seqtk |
|
https://github.com/lh3/seqtk |
seqyclean |
|
https://github.com/ibest/seqyclean |
Seroba |
- 1.0.0
- 1.0.2
- 1.0.2_wslh_signed
|
https://github.com/sanger-pathogens/seroba |
SerotypeFinder |
|
https://bitbucket.org/genomicepidemiology/serotypefinder/ |
Shovill |
|
https://github.com/tseemann/shovill |
SISTR |
|
https://github.com/phac-nml/sistr_cmd |
SKESA |
- 2.3.0
- 2.4.0 (
gfa_connector & kmercounter included)
|
https://github.com/ncbi/SKESA |
Snippy |
|
https://github.com/tseemann/snippy |
snp-dists |
|
https://github.com/tseemann/snp-dists |
SNP-sites |
|
https://github.com/sanger-pathogens/snp-sites |
SPAdes |
- 3.8.2
- 3.12.0
- 3.13.0
- 3.14.0
- 3.14.1
|
https://github.com/ablab/spades http://cab.spbu.ru/software/spades/ |
SRA-toolkit |
|
https://github.com/ncbi/sra-tools |
Staramr |
|
https://github.com/phac-nml/staramr |
TipToft |
|
https://github.com/andrewjpage/tiptoft |
Trimmomatic |
|
http://www.usadellab.org/cms/?page=trimmomatic |
Trycycler |
|
https://github.com/rrwick/Trycycler |
Unicycler |
|
https://github.com/rrwick/Unicycler |
VADR |
|
https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) https://github.com/ncbi/vadr |
VIBRANT |
|
https://github.com/AnantharamanLab/VIBRANT |
VIGOR4 |
|
https://github.com/JCVenterInstitute/VIGOR4 |
wtdbg2 |
|
https://github.com/ruanjue/wtdbg2 |