bacterial-genome-analysis
There are 1 repository under bacterial-genome-analysis topic.
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nf-core / bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Language:Nextflow 50paulstothard / cgview
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
Language:Java 39The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
Language:Perl 29LaborBerlin / score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
Language:Python 24- Language:Python 21
npavlovikj / ProkEvo
ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.
Language:Jupyter Notebook 16ZoyavanMeel / ORCA
Origin of Chromosomal Replication Assessment. Python tool for the analysis of circular bacterial DNA sequences in order to find their origin of replication.
Language:Python 14Sudaraka88 / LDWeaver
Genomewide Epistasis Analysis on Bacteria
Language:R 12deepomicslab / LocalHGT
Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.
Language:Python 11- Language:Nextflow 7
jime-sg / deleat
DELEAT is a bioinformatic analysis pipeline for the design of large-scale genome deletions in bacterial genomes.
Language:Python 6dbespiatykh / RDscan
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
Language:Python 5hzi-bifo / seq2geno
Reproducible and comprehensive sequence analyses for single-species bacterial dataset
Language:Tcl 2- Computer-vision-in-the-service-of-bacteriology
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.
Language:Jupyter Notebook 2 gauravcodepro / evolutionary-rate-analyer
R approach to analyze evolutionary phylogenomics
Language:R 1analyzing bacterial genome based ontologies and phylogenomics informativeness
Language:Python 1jimmlucas / wgs-metasociomic
WGS- Metasociomic- analysing bacterial social interactions in metagenomes of longitudinally collected samples of human microbiomes
Language:Nextflow 1Mister-Teapot / OriC_Finder
Python scripts that predict and plot the location of the origin of replication (oriC) of circular bacterial genomes based on Z-curve analysis, GC-skew analysis. and certain gene locations
Language:Python 1- GCskewAnalyzer
The1stMartian / GCskewAnalyzer
Analyzes the GC skew of bacterial chromosomes using multiple calculations. Outputs a data frame of GC skew values and wiggle files for visualization.
Language:Python 1 vborincenturion / feeds
Food wastE biopEptiDe claSsifier: from microbial genome to biopeptides function
Language:Python 1AaronFeller / Cinful_v2
HMMER-based microcin search using full microcin sequences and double-glycine signal region.
Language:Jupyter Notebook 0francesccoll / assembly_pipeline
Pipeline for de novo assembly of bacterial genomes from paired-end Illumina reads
Language:Python 0MaryAgopian / Variant_Barcoding_M.orygis
Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.
Language:R 0PauloCambranis / QS-Check
A Bash script that automates the search in bacterial genomes for LuxR and LuxI -like proteins. These are important components for Quorum Sensing in bacteria
Language:Shell 0pmenzel / ont-assembly-snake-MIT
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
Language:Python 0Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
Language:Python 0PriyaLakr / coreGenomePhylogeny
Script to design core genome phylogeny using bacterial genome assemblies
Language:Shell 0the-alquemist / GMI-PAN
Bacterial plasmid annotation pipeline
Language:Python 0bacterial genome deep learning using keras
Language:Pythongenome assembler for cleaning, mapping and assembling genomes.
Language:Shellgenome annotation analyzer for the microbiome analysis
Language:Pythonpangenome metagenomics normalizer for gene annotations specifically gene ontologies.
Language:Pythonfrom trinity assembly to deep learning.
Language:Pythonmcn3159 / meet-the-neighbors
Medium scale identification of genomic neighbors in bacterial genomes
Language:Python
