Molecular Microbiology and Infection Unit

Sponsored OSS

Community Organization

Faculty of Medicine

Lisbon

Displaying 1 to 25 of 38 repositories

ummidock/chewbbaca

10K+

1

By Faculty of Medicine

Updated 7 months ago
Docker image of the chewBBACA software for cg/wgMLST
Data Science
ummidock/agc

20

0

By Faculty of Medicine

Updated a year ago
Assembled Genomes Compressor.
Data Science
Machine Learning & AI
ummidock/skani

15

1

By Faculty of Medicine

Updated a year ago
Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.
Data Science
Languages & Frameworks
ummidock/abricate

425

0

By Faculty of Medicine

Updated a year ago
Mass screening of contigs for antimicrobial and virulence genes
Data Science
Security
ummidock/mlst

237

0

By Faculty of Medicine

Updated a year ago
Scan contig files against PubMLST typing schemes
Data Science
Machine Learning & AI
ummidock/innuca

1.0K

0

By Faculty of Medicine

Updated 2 years ago
INNUENDO pipeline for quality control of reads and de novo assembly
Data Science
Machine Learning & AI
ummidock/midas_metagenomics

116

0

By Faculty of Medicine

Updated 4 years ago
MIDAS estimates strain-level genomic variation from metagenomic data
Data Science
Machine Learning & AI
ummidock/seq_typing

1.9K

0

By Faculty of Medicine

Updated 4 years ago
seq_typing - Determines which reference sequence is more likely to be present in a given sample
Data Science
Machine Learning & AI
ummidock/prokka

1.5K

0

By Faculty of Medicine

Updated 4 years ago
Prokka annotates bacterial, archaeal and viral genomes
Data Science
Languages & Frameworks
ummidock/ipyrad

57

0

By Faculty of Medicine

Updated 5 years ago
Interactive toolkit for assembly and analysis of restriction-site associated genomic data sets
Data Science
Machine Learning & AI
ummidock/stacks

32

0

By Faculty of Medicine

Updated 5 years ago
Stacks is a software for building loci from short-read sequences
Data Science
Machine Learning & AI
ummidock/meningotype

82

0

By Faculty of Medicine

Updated 5 years ago
In silico typing of Neisseria meningitidis contigs
Data Science
Machine Learning & AI
ummidock/snippy_tseemann

212

0

By Faculty of Medicine

Updated 5 years ago
Docker container with Snippy software
Data Science
Machine Learning & AI
ummidock/spades

159

0

By Faculty of Medicine

Updated 5 years ago
St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
Data Science
Integration & Delivery
ummidock/blast_binaries

284

0

By Faculty of Medicine

Updated 5 years ago
Blast+ for LOBO cluster performance testing
Data Science
Databases & Storage
ummidock/rpinecone

33

0

By Faculty of Medicine

Updated 6 years ago
rPinecone defines sub-lineages within a bacterial clonal expansion via a phylogenetic tree.
Data Science
Languages & Frameworks
Machine Learning & AI
ummidock/harvest_parsnp

103

1

By Faculty of Medicine

Updated 6 years ago
Parsnp aligns the core genome of hundreds of bacterial genomes within a few minutes to few hours
Data Science
Machine Learning & AI
ummidock/ubuntu_base

113

0

By Faculty of Medicine

Updated 6 years ago
Docker image with basic Ubuntu tools
Integration & Delivery
Operating Systems
Security
ummidock/emm_typing_admiralenola

58

0

By Faculty of Medicine

Updated 6 years ago
Typing of the emm gene of Streptococcus pyogenes (and other Streptococci)
Data Science
Languages & Frameworks
ummidock/seqsero2

137

0

By Faculty of Medicine

Updated 7 years ago
SeqSero2 is a pipeline for Salmonella serotype determination from raw reads or genome assemblies
Data Science
Machine Learning & AI
ummidock/getseqena

245

1

By Faculty of Medicine

Updated 7 years ago
Get fastq files from ENA using Run IDs
Data Science
Machine Learning & AI
ummidock/breseq

2.3K

0

By Faculty of Medicine

Updated 7 years ago
breseq is a pipeline for finding mutations relative to a reference sequence in NGS data
Data Science
Machine Learning & AI
ummidock/assemblerflow_base

313

0

By Faculty of Medicine

Updated 7 years ago
Base image for assemblerflow templates
Data Science
Languages & Frameworks
ummidock/skesa

111

0

By Faculty of Medicine

Updated 7 years ago
Strategic Kmer Extension for Scrupulous Assemblies
Data Science
Integration & Delivery
Machine Learning & AI
ummidock/patho_typing

1.7K

0

By Faculty of Medicine

Updated 7 years ago
In silico pathogenic typing directly from raw Illumina reads
Data Science
Machine Learning & AI