andersen-lab / ivarLinks
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
☆125Updated 2 weeks ago
Alternatives and similar repositories for ivar
Users that are interested in ivar are comparing it to the libraries listed below
Sorting:
- snipit: summarise snps relative to your reference sequence☆164Updated 3 months ago
- The ARTIC field bioinformatics pipeline☆125Updated last month
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated last year
- "Reads to report" for public health and clinical microbiology☆141Updated last year
- BSR-Based Allele Calling Algorithm☆149Updated 3 weeks ago
- Foreign Contamination Screening caller scripts and documentation☆135Updated 5 months ago
- a tool for designing primer panels for multiplex PCR.☆105Updated last year
- Long-read mock community experiments☆106Updated 3 years ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆153Updated 4 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆140Updated last year
- DDBJ Fast Annotation and Submission Tool☆82Updated 3 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆167Updated last week
- ☆208Updated 3 weeks ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆115Updated last year
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Updated 2 years ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆140Updated last week
- Benchmarking of long-read assembly tools for bacterial whole genomes☆173Updated 4 years ago
- ☆143Updated last year
- A fast whole-genome aligner based on de Bruijn graphs☆153Updated last month
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆204Updated last year
- SKESA assembler☆122Updated 10 months ago
- OPERA-MS - Hybrid Metagenomic Assembler☆97Updated 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…☆146Updated 4 months ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆124Updated last year
- DAS Tool☆156Updated last year
- Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics☆193Updated last month
- HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.☆136Updated last year
- Ultra-fast preprocessing and quality control for long-read sequencing data☆174Updated last month
- Get assembly statistics from FASTA and FASTQ files☆122Updated 2 years ago
- Convert various sequence formats to FASTA☆138Updated 3 years ago