treangenlab / OlivarLinks
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
☆33Updated 3 weeks ago
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.☆59Updated 8 months ago
- Remove human reads from a sequencing run☆45Updated last week
- Fast viral consensus genome reconstruction☆25Updated 5 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- A novel method for sequence similarity estimation☆28Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 3 months ago
- ☆30Updated 2 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Updated 3 weeks ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 9 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆44Updated 3 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 4 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Updated 2 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 4 months ago
- Colinear block visualisation tool☆31Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 3 months ago
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- strain-level analysis tools☆39Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆33Updated last week
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated last week
- Library of sketching functions used by PopPUNK☆31Updated 8 months ago
- Genome size estimation from long read overlaps☆74Updated last week
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆35Updated last week
- ♥ Fast and Accurate Estimation of Evolutionary Distances☆29Updated 7 months ago
- Correcting errors in noisy long reads using variation graphs☆50Updated 3 years ago