treangenlab / lemurLinks
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
☆25Updated 4 months ago
Alternatives and similar repositories for lemur
Users that are interested in lemur 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
- Microbial agile accurate SNP Typer☆29Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 8 months ago
- ☆24Updated 10 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 4 months ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- Plasmid analysis using rearrangement distances☆48Updated 3 months ago
- Recombination-free trees☆62Updated 3 months ago
- viralFlye pipeline☆18Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 4 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated last week
- Intra-species bacterial contamination detection☆25Updated 9 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated last week
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 4 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- MAGScoT - a MAG scoring and refinement tool☆39Updated last year
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years 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☆29Updated 9 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆53Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago