artic-network / fieldbioinformaticsLinks
The ARTIC fieldbioinformatics pipeline
☆127Updated last month
Alternatives and similar repositories for fieldbioinformatics
Users that are interested in fieldbioinformatics are comparing it to the libraries listed below
Sorting:
- "Reads to report" for public health and clinical microbiology☆141Updated last year
- snipit: summarise snps relative to your reference sequence☆162Updated 2 months ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated 2 years ago
- Foreign Contamination Screening caller scripts and documentation☆151Updated 8 months ago
- A fast whole-genome aligner based on de Bruijn graphs☆153Updated 5 months ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆172Updated 4 years ago
- Long-read mock community experiments☆104Updated 4 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆130Updated last week
- A tool for generating consensus long-read assemblies for bacterial genomes☆203Updated last month
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆145Updated 3 months ago
- OPERA-MS - Hybrid Metagenomic Assembler☆100Updated last year
- ☆80Updated 5 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆145Updated this week
- ☆220Updated this week
- DDBJ Fast Annotation and Submission Tool☆83Updated 2 months ago
- ☆150Updated last year
- ONT assembly and Illumina polishing pipeline☆89Updated 5 years ago
- 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…☆148Updated 2 months ago
- BSR-Based Allele Calling Algorithm☆147Updated 3 weeks ago
- a short-read polishing tool for long-read assemblies☆196Updated 2 months ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆113Updated 2 years ago
- Nanopore data assembler☆162Updated 3 years ago
- Metagenomic classification of long-read sequencing data☆96Updated 2 weeks ago
- Interactive quality assessment of genome assemblies☆114Updated 2 weeks ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆117Updated last year
- Read Until client library for Nanopore Sequencing☆107Updated last year
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆208Updated last year
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆46Updated 3 months ago
- Get assembly statistics from FASTA and FASTQ files☆124Updated 2 years ago
- ☆222Updated 10 months ago