tomdeman-bio / Sequence-scripts
Random utility scripts for genomics data
☆12Updated 3 years ago
Alternatives and similar repositories for Sequence-scripts:
Users that are interested in Sequence-scripts are comparing it to the libraries listed below
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆31Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Intra-species bacterial contamination detection☆24Updated last month
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated last month
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Advanced metagenomic Sequence Analysis in R☆15Updated 6 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- frame-shift correction for long-read (meta)genomics☆32Updated last year
- ☆36Updated 2 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆31Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 3 months ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆19Updated 8 years ago
- Calculates the lowest common ancestors of each query sequence in a Blast result☆31Updated 7 years ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆21Updated 7 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Gene-flank analysis tool☆26Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 5 years ago
- workflows for offline analysis of 16S rRNA Nanopore data☆12Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- INC-Seq: Accurate single molecule reads using nanopore sequencing☆13Updated 4 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆60Updated 4 years ago