amandawarr / LiloLinks
Stitch together Nanopore tiled amplicon data without polishing a reference
☆17Updated 2 years ago
Alternatives and similar repositories for Lilo
Users that are interested in Lilo are comparing it to the libraries listed below
Sorting:
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing☆19Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 weeks ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 months ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 5 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Updated 3 weeks ago
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Updated 3 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- ☆14Updated 4 years ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆49Updated 2 weeks ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 6 months ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Updated 2 years ago
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Assembly of Nanopore Sequencing☆17Updated last month
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Updated last year
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆28Updated last week
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Updated 3 years ago
- Recombination-free trees☆63Updated 5 months ago
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆18Updated 2 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Updated last year
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆26Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Updated 10 months ago
- Predict plasmids from uncorrected long read data☆41Updated 3 months ago