josephpetrone / RESCUE
Resolving Species Level Classification Using Emu
☆12Updated 9 months ago
Alternatives and similar repositories for RESCUE:
Users that are interested in RESCUE are comparing it to the libraries listed below
- Genome size estimation from long read overlaps☆51Updated 3 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 8 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Classify metagenomic contigs as eukaryotic or prokaryotic☆33Updated 2 years ago
- Remove human reads from a sequencing run☆38Updated 5 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated 2 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 8 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆32Updated 3 months ago
- Bacterial GWAS analysis☆37Updated 2 weeks ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 8 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated 2 weeks ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Calculate assocations between genes and traits☆23Updated 2 weeks ago
- MAGScoT - a MAG scoring and refinement tool☆32Updated 5 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 5 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated 11 months ago
- Colinear block visualisation tool☆30Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆33Updated last month
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆37Updated 3 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- MAG Circularization Method☆33Updated 2 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 5 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆27Updated last month
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago