metagenlab / assembly_finderLinks
snakemake-powered cli to download genomes using NCBI datasets
☆14Updated 5 months ago
Alternatives and similar repositories for assembly_finder
Users that are interested in assembly_finder are comparing it to the libraries listed below
Sorting:
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 8 months ago
- ☆10Updated 2 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last month
- ☆23Updated 4 months ago
- software to identify primers that can distinguish genomes☆21Updated 5 months ago
- Calculate assocations between genes and traits☆23Updated 3 months ago
- Genome size estimation from long read overlaps☆57Updated 2 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆28Updated 8 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 11 months ago
- ☆20Updated 3 weeks ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 11 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Interpretative standards for AMR genotypes☆21Updated 2 weeks ago
- Assembly based core SNP alignments☆7Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last week
- Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!☆33Updated last week
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 3 years ago
- Organism-specific interpretation of AMR genotypes☆13Updated last year
- Plasmid analysis using rearrangement distances☆42Updated last month
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- MAGScoT - a MAG scoring and refinement tool☆35Updated 8 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Bacterial GWAS analysis☆40Updated last month
- Intra-species bacterial contamination detection☆25Updated 4 months ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year