treangenlab / OlivarLinks
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
☆28Updated this week
Alternatives and similar repositories for Olivar
Users that are interested in Olivar are comparing it to the libraries listed below
Sorting:
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 4 months ago
- Genome size estimation from long read overlaps☆59Updated 2 weeks ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆32Updated last week
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆46Updated last week
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆17Updated 2 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- Microbial agile accurate SNP Typer☆30Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- Population analysis PIPEline 🛠🧬☆20Updated 3 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆41Updated 3 weeks ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆26Updated 3 weeks ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 months ago
- UPHL's Reference Free Pipeline☆26Updated this week
- Fast viral consensus genome reconstruction☆23Updated last month
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆37Updated 2 months ago
- Library of sketching functions used by PopPUNK☆31Updated 4 months ago
- Resolving Species Level Classification Using Emu☆14Updated last year
- Remove human reads from a sequencing run☆40Updated last week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆37Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆76Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated last week
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 5 months ago