iqbal-lab-org / pling
Plasmid analysis using rearrangement distances
☆31Updated 3 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☆19Updated 5 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Genome size estimation from long read overlaps☆49Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated last week
- viralFlye pipeline☆18Updated 6 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- Fast and space-efficient taxonomic classification of long reads☆43Updated this week
- Genomewide Epistasis Analysis on Bacteria☆14Updated 5 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Calculate assocations between genes and traits☆23Updated 4 months ago
- ☆13Updated last month
- Recombination-free trees☆57Updated last year
- MAGScoT - a MAG scoring and refinement tool☆31Updated 4 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆22Updated 3 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆26Updated 4 months ago
- software to identify primers that can distinguish genomes☆21Updated last month
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated last week
- Fast viral consensus genome reconstruction☆22Updated 2 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 8 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆24Updated last week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆30Updated 6 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Colinear block visualisation tool☆30Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 10 months ago