Geo-omics / scriptsLinks
Metagenomic pipeline and other general scripts used in the lab.
☆36Updated last year
Alternatives and similar repositories for scripts
Users that are interested in scripts are comparing it to the libraries listed below
Sorting:
- Toolkit for preparing genomes for submission to NCBI☆29Updated 4 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 5 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆68Updated 7 years ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆77Updated 9 years ago
- Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …☆47Updated 3 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Rank-based Gene Ontology analysis of gene expression data☆43Updated 3 years ago
- ☆35Updated 2 years ago
- Visualize whole genome alignments as linear maps☆74Updated 2 weeks ago
- Automatically exported from code.google.com/p/prottest3☆37Updated 8 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆63Updated 5 years ago
- ☆23Updated 7 years ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆66Updated 2 years ago
- Synteny Imager☆65Updated last month
- A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assembli…☆51Updated last year
- ☆37Updated 3 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 7 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 5 years ago
- A statistical framework for ploidy estimation using NGS short-read data☆62Updated 7 years ago
- Scripts and libraries for Environmental Genomics☆38Updated 11 months ago
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Updated last year
- An efficient way to convert gff3 annotation files into EMBL format ready to submit.☆66Updated 6 months 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
- ☆53Updated 4 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmo…☆17Updated 3 years ago
- Automated de novo assembly of whole chloroplast genomes.☆48Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- Workflow for detecting genome-wide horizontal gene transfers☆10Updated 7 years ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆33Updated 2 years ago