Projects in Awesome Lists tagged with bacterial-genomes

https://github.com/tseemann/prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

bacterial-genomes functional-assignment gene-finding genome-annotation

Last synced: 13 Nov 2024

https://github.com/oschwengers/bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

annotation bacteria bacterial-genomes bioinformatics genome-annotation mag metagenome-assembled-genomes microbial-genomics plasmids

Last synced: 19 Dec 2024

https://github.com/bactopia/bactopia

A flexible pipeline for complete analysis of bacterial genomes

bacterial-genomes bioconda conda fastqs nextflow

Last synced: 13 Nov 2024

https://github.com/snitkin-lab-umich/prewas

R package to perform data pre-processing for more informative bacterial GWAS

bacterial-genomes gwas gwas-tools microbiology r r-package

Last synced: 14 Oct 2024

https://github.com/mbhall88/thesis

My PhD thesis

bacterial-genomes basecalling bioinformatics drug-resistance-prediction genome-graphs nanopore-sequencing phd-thesis transmission-clustering tuberculosis

Last synced: 13 Oct 2024

https://github.com/xx19941215/batch-shovill-assemblies

shovill批量执行脚本 Batch Shovill can help you execute shovill batch assemblies.

bacterial-genomes functional-assignment gene-finding genome-annotation shovill

Last synced: 17 Dec 2024

https://github.com/notthestallion/computer-vision-in-the-service-of-bacteriology

Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

bacteria bacterial bacterial-database bacterial-genome-analysis bacterial-genomes bash computer-vision learning opencv

Last synced: 13 Nov 2024

https://github.com/xx19941215/batch-prokka-assemblies

Prokka批量执行脚本 Batch Prokka can help you execute prokka batch assemblies.

bacterial-genomes functional-assignment gene-finding genome-annotation prokka

Last synced: 17 Dec 2024

https://github.com/clavellab/genome-assembly

A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in the Clavel Lab

bacterial-genomes genome-assembly snakemake snakemake-workflows

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/ko-phylogenomics

analyzing bacterial genome based ontologies and phylogenomics informativeness

bacterial-genome-analysis bacterial-genomes geneontology genome-annotation ontologies ontology plant plantgenomes

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/pangenomes-metagenomes

a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads

bacterial-genomes bioinformatics metagenomes metagenomics-data pangenomics pangraphs

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/domain-analyzer

This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. I used a mapping dataframe approach to make it faster rather than looping it over and over.

bacterial-genome-analysis bacterial-genomes domains functional-programming functionaldomains fungal-genomes fungaleffectors interproscan plantgenomes protein-sequence protein-structure proteindomains

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/evolutionary-rate-analyer

A R function for the analysis of the evolutionary rates from the fasta files, and uses the ka/ks and the dn/ds and plots the evolutionary rates.

bacterial-genome-analysis bacterial-genomes bioinformatics evolution evolutionary-computation fungal-genomes fungal-metagenomics plantgenomics rprogramming

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/bacterial-site-checker

A faster implementation of the string search for the check of the insertion elements and the CRISPR sites if present in the genome string and then clip those insertion sites and get a clean genome.

bacterial-genomes bioinformatics fungalgenomics insertionelement sitesplicer

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/bacterial-keras

A keras implementation of machine learning for bacterial genomes, takes a fasta file and the annotation features and the genes you want to train the keras model

bacterial-genome-analysis bacterial-genomes keras machinelearning

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/ontology-annotation-count

a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis

bacterial-genome-analysis bacterial-genomes genome genome-analysis genome-annotation genome-sequencing microbiome microbiome-analysis plantgenomes plantgenomics