LaborBerlin / score-assembliesLinks
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
☆26Updated last year
Alternatives and similar repositories for score-assemblies
Users that are interested in score-assemblies are comparing it to the libraries listed below
Sorting:
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Genome size estimation from long read overlaps☆62Updated last month
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 3 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Colinear block visualisation tool☆31Updated last year
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆11Updated 4 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 4 months ago
- ZGA prokaryotic genome assembly and annotation pipeline☆13Updated last year
- Intra-species bacterial contamination detection☆25Updated 8 months ago
- Predict plasmids from uncorrected long read data☆41Updated 5 years ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated 2 weeks ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Recombination-free trees☆60Updated last month
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆16Updated 7 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Organism-specific interpretation of AMR genotypes☆14Updated last year
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 7 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Order and orientation of complete bacterial genomes☆29Updated 3 months ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 3 years ago
- Calculate assocations between genes and traits☆28Updated 7 months ago