LanLab / ShigEiFinderLinks
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
☆12Updated 2 years ago
Alternatives and similar repositories for ShigEiFinder
Users that are interested in ShigEiFinder are comparing it to the libraries listed below
Sorting:
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- ☆10Updated 9 months ago
- Finding regions of similarity between plasmids☆16Updated 3 years ago
- Organism-specific interpretation of AMR genotypes☆15Updated last year
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Updated 4 years ago
- ☆14Updated 4 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆12Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 6 months ago
- Visualize microbial evolution at the SNP level!☆15Updated 5 months ago
- software to identify primers that can distinguish genomes☆20Updated 3 weeks ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Updated 2 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆12Updated 3 weeks ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆16Updated 5 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 3 years ago
- Parallel/Homoplasic SNP Finder☆21Updated 2 years ago
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆17Updated last month
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Updated 3 months ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated last week
- ☆24Updated 3 weeks ago
- Intra-species bacterial contamination detection☆25Updated 11 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated 2 months ago
- UPHL's Reference Free Pipeline☆27Updated 2 months ago