chrisgulvik

genomics_scripts

c-SSTAR

CLI Sequence Search Tool for Antimicrobial Resistance

mer-freq

phylogenetics_scripts

SPANDx

SPANDx - Comparative genomics for next-generation haploid sequence data

UnivaGridEngine_UGE_cluster_scripts

primarily wrapper scripts to make use of the computing cluster's UGE scheduler

AR_Bank_scripts

batch_MLST_of_species

chewBBACA

BSR-Based Allele Calling Algorithm

ClonalFrameML_scripts

scripts for inferring recombination sites with ClonalFrameML

CSIS

Code Safety Inspection Service

bg-wf-paired-end-illumina-assembly

pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data

De-MetaST

De-MetaST-BLAST

deepvariant

Please consider using/contributing to https://github.com/nf-core/sarek

gustle

find exactly matching contigs in a genome

minknow_api

Protobuff and gRPC specifications for the MinKNOW API

minknow_lims_interface

Protobuff and gRPC specifications for the MinKNOW LIMS Interface

naughty-binfie-files

pima

Plasmid and antimicrobial resistance pipeline

protobuf

Protocol Buffers - Google's data interchange format

pyminknow

Mock minKNOW gRPC server

read_until_api

Read Until client library for Nanopore Sequencing

sars-cov-2-genomic-dashboards

genomic dashboards for visualizing SARS-CoV-2 genomic analyses

scripts

misc scripts

Vagococcus

wf-aai

NextFlow workflow for comparing 2 or more proteomes with Average Amino acid Identity (AAI)

wf-ani

NextFlow workflow for comparing 2 or more genomes with Average Nucleotide Identity (ANI)

wf-assembly-snps

wf-paired-end-illumina-assembly

Trim, assemble, and annotate paired-end Illumina sequences.