USDA-VS / GenoFLULinks
Influenza data pipeline to automate genotyping assignment
☆37Updated 2 weeks ago
Alternatives and similar repositories for GenoFLU
Users that are interested in GenoFLU are comparing it to the libraries listed below
Sorting:
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated 2 weeks ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated last month
- Recombination-free trees☆60Updated 2 months ago
- Calculate assocations between genes and traits☆28Updated 7 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated last week
- Intra-species bacterial contamination detection☆25Updated 8 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Bifrost graph gene caller.☆95Updated last month
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Bacterial GWAS analysis☆45Updated this week
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆42Updated 3 weeks ago
- Genome size estimation from long read overlaps☆62Updated this week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Split Kmer Analysis☆65Updated 3 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Updated 2 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆64Updated this week
- Predict plasmids from uncorrected long read data☆41Updated 5 years ago
- Discover and annotate the virome☆53Updated 2 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 4 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 7 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆31Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 6 months ago
- Code Safety Inspection Service☆20Updated 3 years ago