ABRicate |
- 0.8.7
- 0.8.13
- 0.8.13s (+serotypefinder db)
- 0.9.8
- 1.0.0
|
https://github.com/tseemann/abricate |
any2fasta |
|
https://github.com/tseemann/any2fasta |
ARIBA |
|
https://github.com/sanger-pathogens/ariba |
artic-ncov2019 |
|
https://github.com/artic-network/fieldbioinformatics |
artic-ncov2019-epi2me |
|
https://github.com/epi2me-labs/wf-artic |
artic-ncov2019-medaka |
|
https://github.com/artic-network/artic-ncov2019 |
artic-ncov2019-nanopolish |
|
https://github.com/artic-network/artic-ncov2019 |
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/ https://github.com/arq5x/bedtools2 |
berrywood-report-env |
|
none |
bowtie2 |
|
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://github.com/BenLangmead/bowtie2 |
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 |
datasets-sars-cov-2 |
|
https://github.com/CDCgov/datasets-sars-cov-2 |
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 |
fastq-scan |
|
https://github.com/rpetit3/fastq-scan |
Filtlong |
|
https://github.com/rrwick/filtlong |
Flye |
|
https://github.com/fenderglass/Flye |
Freyja |
|
https://github.com/andersen-lab/Freyja |
GAMBIT |
|
https://github.com/hesslab-gambit/gambit |
GAMMA |
|
https://github.com/rastanton/GAMMA/ |
hmmer |
|
http://hmmer.org/ |
htslib |
|
https://www.htslib.org/ |
iqtree |
|
http://www.iqtree.org/ |
iqtree2 |
|
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
- 1.3.1
|
https://github.com/andersen-lab/ivar |
Kleborate |
|
https://github.com/katholt/Kleborate/ https://github.com/katholt/Kaptive/ |
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)
- 2.1.2 (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 |
minipolish |
|
https://github.com/rrwick/Minipolish |
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
- 3.10.1
- 3.10.5
- 3.10.16
- 3.10.20
|
https://github.com/ncbi/amr |
OrthoFinder |
|
https://github.com/davidemms/OrthoFinder |
Pangolin |
Pangolin version & pangoLEARN data release date - 1.1.14
- 2.0.4 & 2020-07-20
- 2.0.5 & 2020-07-20
- 2.1.1 & 2020-12-17
- 2.1.3 & 2020-12-17
- 2.1.6 & 2021-01-06
- 2.1.7 & 2021-01-11
- 2.1.7 & 2021-01-20
- 2.1.8 & 2021-01-22
- 2.1.10 & 2021-02-01
- 2.1.11 & 2021-02-01
- 2.1.11 & 2021-02-05
- 2.2.1 & 2021-02-06
- 2.2.2 & 2021-02-06
- 2.2.2 & 2021-02-11
- 2.2.2 & 2021-02-12
- 2.3.0 & 2021-02-12
- 2.3.0 & 2021-02-18
- 2.3.0 & 2021-02-21
- 2.3.2 & 2021-02-21
- 2.3.3 & 2021-03-16
- 2.3.4 & 2021-03-16
- 2.3.5 & 2021-03-16
- 2.3.6 & 2021-03-16
- 2.3.6 & 2021-03-29
- 2.3.8 & 2021-04-01
- 2.3.8 & 2021-04-14
- 2.3.8 & 2021-04-21
- 2.3.8 & 2021-04-23
- 2.4 & 2021-04-28
- 2.4.1 & 2021-04-28
- 2.4.2 & 2021-04-28
- 2.4.2 & 2021-05-10
- 2.4.2 & 2021-05-11
- 2.4.2 & 2021-05-19
- 3.0.5 & 2021-06-05
- 3.1.3 & 2021-06-15
- 3.1.5 & 2021-06-15
- 3.1.5 & 2021-07-07-2
- 3.1.7 & 2021-07-09
- 3.1.8 & 2021-07-28
- 3.1.10 & 2021-07-28
- 3.1.11 & 2021-08-09
- 3.1.11 & 2021-08-24
- 3.1.11 & 2021-09-17
- 3.1.14 & 2021-09-28
- 3.1.14 & 2021-10-13
- 3.1.16 & 2021-10-18
- 3.1.16 & 2021-11-04
- 3.1.16 & 2021-11-09
- 3.1.16 & 2021-11-18
- 3.1.16 & 2021-11-25
- 3.1.17 & 2021-11-25
- 3.1.17 & 2021-12-06
- 3.1.17 & 2022-01-05
- 3.1.18 & 2022-01-20
- 3.1.19 & 2022-01-20
- 3.1.20 & 2022-02-02
|
https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/pangoLEARN https://github.com/cov-lineages/pango-designation https://github.com/cov-lineages/scorpio https://github.com/cov-lineages/constellations https://github.com/cov-lineages/lineages (archived) https://github.com/hCoV-2019/pangolin (archived) |
parallel-perl |
|
https://www.gnu.org/software/parallel |
Piggy |
|
https://github.com/harry-thorpe/piggy |
Pilon |
|
https://github.com/broadinstitute/pilon |
PlasmidSeeker |
|
https://github.com/bioinfo-ut/PlasmidSeeker |
pmga |
|
https://github.com/rpetit3/pmga |
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 |
raven |
|
https://github.com/lbcb-sci/raven |
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
- 1.2.1
|
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 |
- 1.1 (perl version)
- 2.0.1 (python version)
|
https://bitbucket.org/genomicepidemiology/serotypefinder/ |
Shovill |
|
https://github.com/tseemann/shovill |
Shovill-se |
|
https://github.com/rpetit3/shovill/tree/v1.1.0se |
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
- 3.15.0
- 3.15.1
- 3.15.2
- 3.15.3
|
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 |
Treemmer |
|
https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) https://github.com/fmenardo/Treemmer |
Trimmomatic |
|
http://www.usadellab.org/cms/?page=trimmomatic https://github.com/usadellab/Trimmomatic |
Trycycler |
|
https://github.com/rrwick/Trycycler |
Unicycler |
|
https://github.com/rrwick/Unicycler |
VADR |
- 1.1
- 1.1.2
- 1.1.3
- 1.2
- 1.2.1
- 1.3 & SARS-CoV-2 models 1.3-1
- 1.3 & SARS-CoV-2 models 1.3-2
- 1.4 & SARS-CoV-2 models 1.3-2
- 1.4.1 & SARS-CoV-2 models 1.3-2
|
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 |
VirSorter2 |
|
https://github.com/jiarong/VirSorter2 |
wtdbg2 |
|
https://github.com/ruanjue/wtdbg2 |