StaPH-B

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Community Organization

State Public Health Bioinformatics Community

Displaying 1 to 25 of 225 repositories

staphb/freyja

100K+

0
Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset

Pulls:

549

Feb 10 to Feb 16

staphb/augur

2.8K

0
Data Science
Machine Learning & AI

Pulls:

0

Feb 3 to Feb 9

staphb/kma

1.0K

0
kma: Rapid and precise k-mer alignment against redundant databases.
Data Science
Integration & Delivery
Machine Learning & AI

Pulls:

7

Feb 10 to Feb 16

staphb/ncbi-datasets

7.6K

0
NCBI Datasets: easily gather data from across NCBI databases
Data Science
Machine Learning & AI

Pulls:

57

Feb 10 to Feb 16

staphb/bbtools

500K+

0
BBTools suite of tools from Joint Genome Institute

Pulls:

507

Feb 10 to Feb 16

staphb/sistr

844

0
Salmonella In Silico Typing Resource (SISTR)

Pulls:

21

Feb 10 to Feb 16

staphb/ncbi-amrfinderplus

50K+

1
Find acquired AMR genes and some point mutations in protein or assembled nucleotide sequences

Pulls:

133

Feb 10 to Feb 16

staphb/mykrobe

5.5K

0
Mykrobe + Genotyphi + Sonneityping for antibiotic resistance prediction, and genotyping
Data Science
Machine Learning & AI

Pulls:

23

Feb 10 to Feb 16

staphb/mlst

100K+

1
Scan contig files against traditional PubMLST typing schemes (tool from T. Seemann)
Data Science
Machine Learning & AI

Pulls:

148

Feb 10 to Feb 16

staphb/pangolin

1M+

3
Software package for assigning SARS-CoV-2 genome sequences to global lineages

Pulls:

284

Feb 10 to Feb 16

staphb/panaroo

1.0K

1
Panaroo: An updated pipeline for pangenome investigation
Data Science
Machine Learning & AI

Pulls:

10

Feb 10 to Feb 16