metagenlab / assembly_finder
snakemake-powered cli to download genomes using NCBI datasets
☆13Updated last week
Alternatives and similar repositories for assembly_finder:
Users that are interested in assembly_finder are comparing it to the libraries listed below
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 4 months ago
- Assembly based core SNP alignments☆7Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆41Updated last month
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 6 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Genome size estimation from long read overlaps☆47Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆55Updated last week
- Calculate assocations between genes and traits☆20Updated 3 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 3 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 6 months ago
- Plasmid analysis using rearrangement distances☆31Updated 2 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated last year
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 2 years ago
- ☆13Updated 7 years ago
- Bacterial GWAS analysis☆35Updated last month
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- ☆13Updated last week
- MAGScoT - a MAG scoring and refinement tool☆31Updated 3 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14Updated 8 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆29Updated 5 months ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆10Updated 2 years ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆18Updated 2 years ago
- Intra-species bacterial contamination detection☆24Updated 2 months ago
- Code used to analyse and plot metadata of metagenomic binning tools☆11Updated 5 months ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆32Updated last year
- CFSAN Shigella Typing Pipeline☆14Updated last year