jaleezyy / covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
☆30Updated last month
Related projects ⓘ
Alternatives and complementary repositories for covid-19-signal
- Influenza genome analysis Nextflow workflow☆22Updated last week
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆26Updated last year
- ☆27Updated last year
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆32Updated last week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆26Updated 4 months ago
- Fast and space-efficient taxonomic classification of long reads☆42Updated 2 weeks ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆44Updated last year
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆23Updated this week
- Recombination-free trees☆56Updated last year
- Influenza genome analysis Nextflow workflow☆16Updated last week
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆19Updated last year
- ☆19Updated last week
- Find Unique genomic Regions☆29Updated last week
- InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..☆29Updated 10 months ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆32Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Updated 3 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 4 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆36Updated 11 months ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆31Updated 11 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated 3 months ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆35Updated 2 weeks ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆17Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆52Updated last year