CFSAN-Biostatistics / snp-pipelineLinks
SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
☆63Updated 2 years ago
Alternatives and similar repositories for snp-pipeline
Users that are interested in snp-pipeline are comparing it to the libraries listed below
Sorting:
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- ☆37Updated 3 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆63Updated 5 years ago
- ☆53Updated 4 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Pipeline to generate NGS reads from a phylogeny☆39Updated 3 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- ☆26Updated 6 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Visualize whole genome alignments as linear maps☆73Updated 3 months ago
- ☆33Updated 4 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆76Updated 9 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆57Updated 2 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆68Updated 7 years ago
- de novo virus assembler of Illumina paired reads☆58Updated 4 years ago
- Toolkit for preparing genomes for submission to NCBI☆29Updated 4 years ago
- A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.☆45Updated 4 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Synteny Imager☆65Updated 3 weeks ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆36Updated 5 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 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
- Conditional Reciprocal Best Blast☆42Updated 8 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆41Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- de.NBI Nanopore Training Course☆20Updated 5 months ago
- Metagenomic binning suite☆29Updated 3 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago