connor-lab / ncov2019-artic-nfLinks
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
☆91Updated last year
Alternatives and similar repositories for ncov2019-artic-nf
Users that are interested in ncov2019-artic-nf are comparing it to the libraries listed below
Sorting:
- The ARTIC fieldbioinformatics pipeline☆125Updated last week
- snipit: summarise snps relative to your reference sequence☆163Updated 4 months ago
- "Reads to report" for public health and clinical microbiology☆140Updated last year
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆126Updated this week
- Long-read mock community experiments☆105Updated 3 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆140Updated last year
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆115Updated last year
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆145Updated 4 months ago
- SKESA assembler☆124Updated 11 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆140Updated 3 weeks ago
- Sorts amplicons from Nanopore sequencing data based on similarity☆39Updated 3 months ago
- DDBJ Fast Annotation and Submission Tool☆82Updated last week
- Foreign Contamination Screening caller scripts and documentation☆138Updated 6 months ago
- A fast whole-genome aligner based on de Bruijn graphs☆152Updated 2 months ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆172Updated 4 years ago
- ☆83Updated 2 years ago
- ☆79Updated 4 years ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆48Updated last year
- A tool for generating consensus long-read assemblies for bacterial genomes☆183Updated 2 weeks ago
- Interactive quality assessment of genome assemblies☆107Updated 4 months ago
- BSR-Based Allele Calling Algorithm☆148Updated 2 weeks ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆111Updated last year
- ONT assembly and Illumina polishing pipeline☆89Updated 4 years ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆46Updated last week
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆51Updated 9 months ago
- OPERA-MS - Hybrid Metagenomic Assembler☆99Updated last year
- A tool for Racon polishing of miniasm assemblies☆77Updated 2 weeks ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated last year
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆127Updated last year
- A pipeline for running AMRfinderPlus and collating results into functional classes☆80Updated last year