harry-thorpe / piggyLinks
Pipeline for analysing intergenic regions in bacteria
☆40Updated 5 years ago
Alternatives and similar repositories for piggy
Users that are interested in piggy are comparing it to the libraries listed below
Sorting:
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Intra-species bacterial contamination detection☆25Updated 6 months ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Recombination-free trees☆59Updated 5 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆76Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆24Updated last year
- Graph-based assembly phasing☆88Updated 4 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- PLSDB pipeline to collect bacterial plasmids from NCBI☆38Updated 10 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆49Updated last month
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- Order and orientation of complete bacterial genomes☆28Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Calculate assocations between genes and traits☆25Updated 5 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆60Updated 6 months ago
- all methods related to Enterobase☆43Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- whole genome MLST analysis☆46Updated 2 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated last month
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated 3 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- MetaCompass: Reference-guided Assembly of Metagenomes☆39Updated 3 weeks ago