nf-core / viralmetagenomeLinks
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
☆27Updated 2 weeks ago
Alternatives and similar repositories for viralmetagenome
Users that are interested in viralmetagenome are comparing it to the libraries listed below
Sorting:
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆60Updated 2 weeks ago
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Updated last year
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Fast and space-efficient taxonomic classification of long reads☆42Updated 4 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Updated last year
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆48Updated 2 weeks ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 6 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 3 years ago
- Bacterial GWAS analysis☆46Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated 2 months ago
- A package to annotate protein sequences☆60Updated 10 months ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- Recombination-free trees☆63Updated 4 months ago
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- strain-level analysis tools☆39Updated last year
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆22Updated last month
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated last week
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆45Updated last week
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆44Updated 9 months ago
- Accurate metagenomi/metatranscriptomic analysis pipeline☆23Updated 4 years ago
- Gene-flank analysis tool☆34Updated last year
- A toolkit for prokaryotic comparative genomics☆51Updated 2 months ago
- ☆26Updated 2 years ago
- Parallelised and automated construction of metagenomic classifier databases of different tools☆20Updated 2 weeks ago
- Influenza genome analysis Nextflow workflow☆24Updated 3 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆41Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆41Updated last month
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Updated 2 years ago
- MAG Circularization Method☆32Updated 2 months ago