staphb

StaPH-B

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State Public Health Bioinformatics Community

Displaying 1 to 25 of 225 repositories

staphb/unicycler

10K+

0

By staphb

Updated 9 hours ago
Hybrid assembly pipeline for bacterial genomes
Data Science
Machine Learning & AI
staphb/freyja

100K+

0

By staphb

Updated 3 days ago
Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset
staphb/usher

38

0

By staphb

Updated 5 days ago
staphb/augur

2.8K

0

By staphb

Updated 5 days ago
Data Science
Machine Learning & AI
staphb/kma

1.0K

0

By staphb

Updated 6 days ago
kma: Rapid and precise k-mer alignment against redundant databases.
Data Science
Integration & Delivery
Machine Learning & AI
staphb/diamond

129

0

By staphb

Updated 6 days ago
staphb/ncbi-datasets

7.7K

0

By staphb

Updated 6 days ago
NCBI Datasets: easily gather data from across NCBI databases
Data Science
Machine Learning & AI
staphb/bakta

3.3K

0

By staphb

Updated 9 days ago
staphb/bbtools

500K+

0

By staphb

Updated 9 days ago
BBTools suite of tools from Joint Genome Institute
staphb/freebayes

10K+

0

By staphb

Updated 13 days ago
staphb/sistr

844

0

By staphb

Updated 14 days ago
Salmonella In Silico Typing Resource (SISTR)
staphb/genoflu

140

0

By staphb

Updated 14 days ago
staphb/ncbi-amrfinderplus

50K+

1

By staphb

Updated 20 days ago
Find acquired AMR genes and some point mutations in protein or assembled nucleotide sequences
staphb/cat

78

0

By staphb

Updated 20 days ago
staphb/stxtyper

164

0

By staphb

Updated 20 days ago
staphb/mykrobe

5.5K

0

By staphb

Updated 20 days ago
Mykrobe + Genotyphi + Sonneityping for antibiotic resistance prediction, and genotyping
Data Science
Machine Learning & AI
staphb/cbird-util

78

0

By staphb

Updated 22 days ago
staphb/mlst

100K+

1

By staphb

Updated a month ago
Scan contig files against traditional PubMLST typing schemes (tool from T. Seemann)
Data Science
Machine Learning & AI
staphb/pangolin

1M+

3

By staphb

Updated a month ago
Software package for assigning SARS-CoV-2 genome sequences to global lineages
staphb/panaroo

1.0K

1

By staphb

Updated a month ago
Panaroo: An updated pipeline for pangenome investigation
Data Science
Machine Learning & AI
staphb/krocus

34

0

By staphb

Updated a month ago
staphb/falco

39

0

By staphb

Updated a month ago
staphb/krona

46

0

By staphb

Updated a month ago