tseemann / scripts
Miscellaneous Perl scripts from 20 years in microbial bioinformatics
☆17Updated 9 months ago
Alternatives and similar repositories for scripts:
Users that are interested in scripts are comparing it to the libraries listed below
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- Bacterial GWAS analysis☆40Updated this week
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated this week
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 6 months ago
- Recombination-free trees☆58Updated 3 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 2 weeks ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Calculate assocations between genes and traits☆23Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆34Updated last month
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 9 months ago
- Gene Absence Presence Identification tool.☆26Updated 3 weeks ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14Updated 11 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated last month
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆32Updated 4 months ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Plasmid analysis using rearrangement distances☆42Updated 5 months ago
- Order and orientation of complete bacterial genomes☆27Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Genome size estimation from long read overlaps☆52Updated last week
- Split Kmer Analysis☆63Updated 2 years ago
- Code Safety Inspection Service☆20Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- BEAV: Bacterial Element Annotation reVamped☆64Updated 5 months ago
- Remove human reads from a sequencing run☆40Updated 6 months ago