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ar_bank_scripts

batch_mlst_of_species

bg-wf-paired-end-illumina-assembly

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

c-sstar

CLI Sequence Search Tool for Antimicrobial Resistance

chewbbaca

BSR-Based Allele Calling Algorithm

clonalframeml_scripts

scripts for inferring recombination sites with ClonalFrameML

csis

Code Safety Inspection Service

de-metast

de-metast-blast

deepvariant

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

genomics_scripts

gustle

find exactly matching contigs in a genome

images

mer-freq

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

phylogenetics_scripts

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

see_snp_neighborhoods

visualize read pileup neighborhoods of genomic and pairwise SNPs

spandx

SPANDx - Comparative genomics for next-generation haploid sequence data

summarize_kraken_data

scripts to summarize output from Kraken, the taxonomic sequence classifier

univagridengine_uge_cluster_scripts

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

usda-vs_public_backport

USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees. In addition virus, mainly influenza, Kraken / Krona and reference guided assembly.

vagococcus