snacktavish / TreeToReadsLinks
Pipeline to generate NGS reads from a phylogeny
☆39Updated 3 years ago
Alternatives and similar repositories for TreeToReads
Users that are interested in TreeToReads are comparing it to the libraries listed below
Sorting:
- Split Kmer Analysis☆65Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- ☆37Updated 3 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Toolkit for preparing genomes for submission to NCBI☆29Updated 4 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated last month
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated 2 weeks ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆76Updated 9 years ago
- Predict plasmids from uncorrected long read data☆41Updated 5 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 5 years ago
- Gene-flank analysis tool☆33Updated 10 months ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Updated last year
- Recombination-free trees☆60Updated last month
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated last week
- ☆53Updated 4 years ago
- Visualize whole genome alignments as linear maps☆73Updated 2 months ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆63Updated 2 years ago
- Phylogenetics between and within hosts at once, all along the genome.☆50Updated last year
- CRyPTIC data processing pipelines☆34Updated last year
- Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.☆69Updated 5 years ago
- ☆36Updated 6 months ago