connor-lab / ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
☆89Updated last year
Related projects ⓘ
Alternatives and complementary repositories for ncov2019-artic-nf
- The ARTIC field bioinformatics pipeline☆116Updated last week
- snipit: summarise snps relative to your reference sequence☆149Updated last week
- Pairwise SNP distance matrix from a FASTA sequence alignment☆127Updated 8 months ago
- SKESA assembler☆112Updated last month
- Long-read mock community experiments☆103Updated 3 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆108Updated 6 months ago
- A fast whole-genome aligner based on de Bruijn graphs☆141Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆118Updated last month
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆107Updated last week
- ONT assembly and Illumina polishing pipeline☆91Updated 3 years ago
- ☆116Updated this week
- Sorts amplicons from Nanopore sequencing data based on similarity☆32Updated last month
- 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…☆129Updated this week
- "Reads to report" for public health and clinical microbiology☆136Updated 8 months ago
- A tool for Racon polishing of miniasm assemblies☆73Updated 3 years ago
- DDBJ Fast Annotation and Submission Tool☆78Updated last month
- ARTIC SARS-CoV-2 workflow and reporting☆49Updated 2 months ago
- ☆151Updated 2 months ago
- Pan-genome wide association studies☆150Updated 5 months ago
- Bioinformatics Pipeline and Visualization resources☆54Updated 2 months ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆117Updated 8 months ago
- ☆76Updated 4 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆93Updated this week
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆48Updated 6 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆71Updated 3 months ago
- Nextflow pipeline for analysis of direct RNA Nanopore reads☆93Updated last month
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆97Updated last year
- Analysis components from Oxford Nanopore Research☆93Updated 2 months ago
- a signal-level demultiplexer for Oxford Nanopore reads☆124Updated 3 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆71Updated 11 months ago