Geo-omics / scriptsLinks
Metagenomic pipeline and other general scripts used in the lab.
☆36Updated 8 months ago
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☆56Updated 4 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☆76Updated 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
- Rank-based Gene Ontology analysis of gene expression data☆42Updated 2 years ago
- A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats☆30Updated 2 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- ☆23Updated 7 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 pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Dual barcode and primer demultiplexing for MinION sequenced reads☆41Updated 2 years ago
- Synteny Imager☆64Updated 2 months ago
- A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt☆31Updated 4 years ago
- An efficient way to convert gff3 annotation files into EMBL format ready to submit.☆62Updated 2 months ago
- Updated Kraken DB install scripts to cope with new-ish NCBI structure☆47Updated 8 years 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
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆54Updated 3 months ago
- Select primer sets for selective whole genome amplification (SWGA)☆32Updated 6 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- ☆53Updated 4 years ago
- ☆35Updated 2 years ago
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 5 months ago
- Visualize whole genome alignments as linear maps☆73Updated 2 months ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Collection of scripts for bacterial genomics☆48Updated 5 years ago
- A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).☆92Updated last year
- Surveillance of pathogens using population genomics and sequencing☆43Updated 3 months ago
- Automatically exported from code.google.com/p/prottest3☆38Updated 7 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆62Updated 5 years ago