pha4ge / pipeline-resourcesLinks
Bioinformatics Pipeline and Visualization resources
☆60Updated 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
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated last week
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- 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
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated last month
- Reference-based consensus creation☆57Updated last week
- A scalable bacterial genome assembly, annotation and analysis pipeline☆75Updated 2 years ago
- Primer schemes for real-time genome epidemiology☆30Updated 2 years ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- de novo virus assembler of Illumina paired reads☆58Updated 4 years ago
- Standard database for the TBProfiler tool☆31Updated 3 months ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Updated 7 months ago
- Microbiome classification pipeline☆65Updated 6 months ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 5 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆39Updated this week
- Split Kmer Analysis☆65Updated 3 years ago
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- Recombination-free trees☆62Updated 3 months ago
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆85Updated 11 months ago
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆52Updated last year
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated 2 weeks ago
- Rapid determination of appropriate reference genomes.☆97Updated 10 months ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- A toolkit for prokaryotic comparative genomics☆51Updated last month
- Gene-flank analysis tool☆34Updated 11 months ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆71Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago