pha4ge / pipeline-resourcesLinks
Bioinformatics Pipeline and Visualization resources
☆55Updated 9 months ago
Alternatives and similar repositories for pipeline-resources
Users that are interested in pipeline-resources are comparing it to the libraries listed below
Sorting:
- ARTIC SARS-CoV-2 workflow and reporting☆51Updated 2 months 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 scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated last year
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆31Updated 3 weeks ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated 10 months ago
- SC2 variant detection and composition pipeline☆17Updated last year
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆99Updated this week
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆41Updated 3 years ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 5 years ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆60Updated 9 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆52Updated this week
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- Bifrost graph gene caller.☆95Updated 9 months ago
- de novo virus assembler of Illumina paired reads☆56Updated 4 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆57Updated 2 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆59Updated last week
- Standard database for the TBProfiler tool☆29Updated last week
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆42Updated 7 months ago
- Micro 612 genomics workshop☆37Updated 4 years ago
- Split k-mer analysis – version 2☆87Updated 4 months ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆49Updated last year
- Influenza genome analysis Nextflow workflow☆22Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆37Updated 3 weeks ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated 2 months ago
- Precise host read removal☆101Updated last week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 11 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆29Updated 2 months ago