iqbal-lab-org / pling
Plasmid analysis using rearrangement distances
☆42Updated 5 months ago
Alternatives and similar repositories for pling:
Users that are interested in pling are comparing it to the libraries listed below
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 2 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- Recombination-free trees☆58Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated this week
- a simple tool for listing conda environments with descriptions☆12Updated 3 weeks ago
- Genome size estimation from long read overlaps☆52Updated last week
- Fast and space-efficient taxonomic classification of long reads☆43Updated last month
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆25Updated this week
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- Calculate assocations between genes and traits☆23Updated last month
- reference-based long read assemblies of bacterial genomes☆48Updated 3 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆34Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆22Updated 3 weeks ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated this week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Bacterial GWAS analysis☆40Updated this week
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated last week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 9 months ago
- Jaeger is a quick and precise tool for detecting phages in sequence assemblies.☆29Updated this week
- plasmidVerify: plasmid contig verification tool☆13Updated 4 years ago
- Intra-species bacterial contamination detection☆25Updated 2 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated last year
- Order and orientation of complete bacterial genomes☆27Updated last year
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago