cov-lineages / lineagesLinks
Resources for calling and describing the circulating lineages of SARS-CoV-2
☆37Updated 4 years ago
Alternatives and similar repositories for lineages
Users that are interested in lineages are comparing it to the libraries listed below
Sorting:
- Classify sequencing reads using MinHash.☆48Updated 5 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36Updated 3 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated 2 months ago
- Benchmark datasets for WGS analysis☆39Updated 5 years ago
- serious constellations of reoccurring phylogenetically-independent origin☆39Updated last year
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Updated last year
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- The Zika bioinformatics pipeline☆36Updated 5 years ago
- A comprehensive pipeline for short read metagenomic data☆24Updated 4 years ago
- ☆8Updated 3 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆37Updated this week
- Amplicon Sequencing Analysis Pipeline☆16Updated 3 weeks ago
- A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies☆37Updated 2 years ago
- SARS-CoV-2 variant calling and consensus assembly pipeline☆25Updated last year
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆59Updated 2 years ago
- Fungal Genome Mapping Pipeline☆19Updated 6 years ago
- blast, shmlast☆22Updated 4 years ago
- Malleable All-seeing Journal Of Research Artifacts☆36Updated 2 years ago
- Database of genomes integrated from the gut microbiome and other environments☆45Updated 2 years ago
- Systematic ProtEin AnnotatoR☆19Updated 8 months ago
- Influenza genome analysis Nextflow workflow☆22Updated 2 months ago
- Remove host contaminants from sequencing files☆9Updated 5 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- REINDEER REad Index for abuNDancE quERy☆58Updated 11 months ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- TAXnomic Profile Aggregation and STAndardisation☆41Updated 7 months ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆27Updated this week