LanLab / ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
☆11Updated last year
Alternatives and similar repositories for ShigEiFinder:
Users that are interested in ShigEiFinder are comparing it to the libraries listed below
- CFSAN Shigella Typing Pipeline☆14Updated last year
- ☆10Updated last week
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Visualize microbial evolution at the SNP level!☆14Updated 5 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆11Updated 3 weeks ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆9Updated 3 years ago
- ☆15Updated 2 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- software to identify primers that can distinguish genomes☆21Updated 3 months ago
- Generate basic stats for an assembly.☆11Updated 2 years ago
- Genome size estimation from long read overlaps☆52Updated last week
- A pipeline for bioinformatics analysis of bacterial genomes☆22Updated 3 weeks ago
- Organism-specific interpretation of AMR genotypes☆10Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 6 months ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated last year
- Intra-species bacterial contamination detection☆25Updated 2 months ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 10 months ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 4 months ago
- Archived - please see updated sccmec tool at link below☆13Updated 7 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Updated last year
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated 11 months ago
- UPHL's Reference Free Pipeline☆26Updated 2 weeks ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆12Updated 7 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Sketch-based surveillance platform☆13Updated 4 months ago
- Plasmid and antimicrobial resistance pipeline☆16Updated 3 months ago