JordyCoolen / easyseq_covid19
Pipeline to automatically analyse SARS-CoV-2 Whole genome sequencing Illumina data obtained using EasySeq SARS-CoV-2/COVID-19 Whole Genome Sequencing kit.
☆15Updated 2 years ago
Alternatives and similar repositories for easyseq_covid19:
Users that are interested in easyseq_covid19 are comparing it to the libraries listed below
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- ASMNGS20 - 2020 Conference Details☆15Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆33Updated 4 months ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate☆30Updated 2 years ago
- ☆52Updated 3 years ago
- A SARS-CoV-2 Mutation Pattern Query Tool☆17Updated 2 years ago
- Harmonization of AMR predictor tool outputs☆25Updated 2 months ago
- Calculate confidence scores from Kraken2 output☆21Updated last year
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆27Updated last week
- ☆26Updated 5 years ago
- Select primer sets for selective whole genome amplification (SWGA)☆32Updated 6 years ago
- A MinION-based pipeline for tracking species biodiversity☆13Updated last year
- Split Kmer Analysis☆63Updated 2 years ago
- InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..☆30Updated last year
- de.NBI Nanopore Training Course☆20Updated 2 years ago
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- Remove lambda phage reads from a fastq file☆29Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Various scripts and recipes for working with nanopore data☆34Updated 8 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated 11 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 9 months ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆17Updated 2 months ago
- rapidly rid reads of horrid humans☆15Updated 3 years ago
- SC2 variant detection and composition pipeline☆17Updated last year
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago