andersen-lab / Freyja
Depth-weighted De-Mixing
☆107Updated this week
Alternatives and similar repositories for Freyja:
Users that are interested in Freyja are comparing it to the libraries listed below
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆134Updated 4 months ago
- snipit: summarise snps relative to your reference sequence☆153Updated 3 weeks ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆119Updated last week
- ☆11Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆116Updated 3 weeks ago
- Foreign Contamination Screening caller scripts and documentation☆122Updated 3 months ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated last year
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆97Updated 2 weeks ago
- BSR-Based Allele Calling Algorithm☆140Updated last week
- Massively parallel phylogenetic placement of genetic sequences☆81Updated 2 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆97Updated 3 weeks ago
- Sorts amplicons from Nanopore sequencing data based on similarity☆34Updated 4 months ago
- "Reads to report" for public health and clinical microbiology☆138Updated 11 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆112Updated 8 months ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆90Updated last year
- ☆129Updated 8 months ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆169Updated last year
- Pairwise SNP distance matrix from a FASTA sequence alignment☆129Updated 11 months ago
- The ARTIC field bioinformatics pipeline☆120Updated last week
- Reorients assembled microbial sequences☆109Updated last week
- SC2 variant detection and composition pipeline☆16Updated last year
- fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads☆45Updated 6 months ago
- DDBJ Fast Annotation and Submission Tool☆79Updated this week
- A toolbox for comparative genomics.☆101Updated 3 years ago
- Find endogenous viral elements in genomes☆11Updated 2 weeks ago
- fast phage annotation program☆155Updated last month
- ☆198Updated 3 weeks ago
- A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…☆59Updated 2 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆182Updated last month
- Making whole bacterial genome sequencing data analysis easy☆103Updated 3 months ago