tseemann / scriptsLinks
Miscellaneous Perl scripts from 20 years in microbial bioinformatics
☆17Updated 11 months ago
Alternatives and similar repositories for scripts
Users that are interested in scripts are comparing it to the libraries listed below
Sorting:
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 8 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last week
- Bacterial GWAS analysis☆40Updated 3 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆28Updated 8 months ago
- Recombination-free trees☆58Updated 3 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 11 months ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 3 years ago
- Calculate assocations between genes and traits☆23Updated 3 months ago
- Genome size estimation from long read overlaps☆57Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last month
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆37Updated 3 weeks ago
- Gene-flank analysis tool☆27Updated 6 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- Gene Absence Presence Identification tool.☆26Updated 2 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆29Updated last month
- Intra-species bacterial contamination detection☆25Updated 4 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 2 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Jaeger is a quick and precise tool for detecting phages in sequence assemblies.☆31Updated this week
- Code Safety Inspection Service☆20Updated 2 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆36Updated 2 months ago
- IslandPath standalone software☆32Updated last year