tseemann / scriptsLinks
Miscellaneous Perl scripts from 20 years in microbial bioinformatics
☆17Updated last year
Alternatives and similar repositories for scripts
Users that are interested in scripts are comparing it to the libraries listed below
Sorting:
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 7 months ago
- Bacterial GWAS analysis☆46Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Recombination-free trees☆62Updated 3 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Calculate assocations between genes and traits☆29Updated 8 months ago
- Interpretative standards for AMR genotypes☆26Updated this week
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated 2 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 4 months ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Predict plasmids from uncorrected long read data☆41Updated last month
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 9 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated this week
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 7 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Gene-flank analysis tool☆34Updated 11 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated this week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated 2 weeks ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆42Updated 2 years ago
- IslandPath standalone software☆34Updated 2 years ago
- zDB: comparative bacterial genomics made easy☆36Updated this week