LanLab / ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
☆11Updated last year
Related projects ⓘ
Alternatives and complementary repositories for ShigEiFinder
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 5 months ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆9Updated 3 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- Intra-species bacterial contamination detection☆22Updated this week
- Targeted Detection and Reconstruction of Plasmids☆19Updated 6 months ago
- Visualize microbial evolution at the SNP level!☆13Updated last week
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆11Updated 2 months ago
- NCBI Pathogen Detection Portal toolkit☆11Updated last year
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆11Updated 8 months ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- frame-shift correction for long-read (meta)genomics☆31Updated 11 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆17Updated 6 months ago
- ☆13Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆28Updated 2 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆11Updated 7 months ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 3 weeks ago
- Plasmid analysis using rearrangement distances☆30Updated last week