harry-thorpe / piggy
Pipeline for analysing intergenic regions in bacteria
☆38Updated 5 years ago
Alternatives and similar repositories for piggy:
Users that are interested in piggy are comparing it to the libraries listed below
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Intra-species bacterial contamination detection☆25Updated last month
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- Recombination-free trees☆57Updated this week
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 11 months ago
- whole genome MLST analysis☆41Updated this week
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 5 months ago
- plasmidVerify: plasmid contig verification tool☆13Updated 4 years ago
- Gene Absence Presence Identification tool.☆26Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Assessing and Improving the quality of metagenomic assemblies☆28Updated 3 years ago
- Order and orientation of complete bacterial genomes☆27Updated last year
- PLSDB pipeline to collect bacterial plasmids from NCBI☆38Updated 5 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- Gene-flank analysis tool☆27Updated 3 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆19Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated 3 weeks ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆33Updated last month
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Strain Resolution ON Graphs☆47Updated last year
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago