pha4ge / pipeline-resourcesLinks
Bioinformatics Pipeline and Visualization resources
☆58Updated last year
Alternatives and similar repositories for pipeline-resources
Users that are interested in pipeline-resources are comparing it to the libraries listed below
Sorting:
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated last year
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated last week
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Collection of scripts for bacterial genomics☆48Updated 5 years ago
- Bifrost graph gene caller.☆95Updated last month
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 4 months ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated 2 months ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆75Updated last year
- k-mer learning materials☆80Updated 8 months ago
- hecatomb is a virome analysis pipeline for analysis of Illumina sequence data☆59Updated last month
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated 6 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆51Updated last year
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆103Updated 7 months ago
- Standard database for the TBProfiler tool☆31Updated 2 months ago
- ☆37Updated 3 years ago
- Gene-flank analysis tool☆33Updated 10 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆38Updated 2 weeks ago
- Primer schemes for real-time genome epidemiology☆30Updated 2 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆56Updated last week
- A tool for removing redundant genomes from a set of assemblies☆77Updated last month
- ☆79Updated this week
- Reference-based consensus creation☆57Updated last week
- Microbiome classification pipeline☆65Updated 5 months ago