CFSAN-Biostatistics / snp-pipeline
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.
☆57Updated last year
Alternatives and similar repositories for snp-pipeline:
Users that are interested in snp-pipeline are comparing it to the libraries listed below
- Filter SAM file for soft and hard clipped alignments☆46Updated 7 months ago
- ☆36Updated 2 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆56Updated last year
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆74Updated 8 years ago
- de.NBI Nanopore Training Course☆19Updated 2 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- de novo virus assembler of Illumina paired reads☆54Updated 3 years ago
- A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt☆30Updated 4 years ago
- ☆52Updated 3 years ago
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆38Updated last month
- catalog for long-read sequencing tools☆32Updated last year
- Synteny Imager☆60Updated 4 months ago
- Visualize whole genome alignments as linear maps☆70Updated 3 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆60Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆43Updated 4 years ago
- Tools for working with second gen assemblies, fasta sequences, etc☆92Updated 8 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆65Updated 6 years ago
- ☆32Updated 4 years ago
- finshingTool☆54Updated 8 years ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…☆52Updated last year
- Various scripts and recipes for working with nanopore data☆34Updated 8 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 3 years ago
- Scripts and programs for the Holt Lab's MinION desktop☆32Updated 4 years ago
- Transcripts annotation and GO enrichment Fisher tests☆26Updated last year
- LRSDAY: Long-read Sequencing Data Analysis for Yeasts☆31Updated 10 months ago