Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: bacterial-genomes
infinity-a11y/PhyloTrace
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
Language: R - Size: 18.9 MB - Last synced: 33 minutes ago - Pushed: about 2 hours ago - Stars: 3 - Forks: 0
nf-core/bacass
Simple bacterial assembly and annotation pipeline
Language: Nextflow - Size: 4.69 MB - Last synced: about 7 hours ago - Pushed: 1 day ago - Stars: 51 - Forks: 35
bactopia/bactopia
A flexible pipeline for complete analysis of bacterial genomes
Language: Nextflow - Size: 48.6 MB - Last synced: about 16 hours ago - Pushed: 10 days ago - Stars: 359 - Forks: 61
gem-pasteur/Integron_Finder
Bioinformatics tool to find integrons in bacterial genomes
Language: F* - Size: 55.9 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 61 - Forks: 22
garcia-nacho/TOP
Bacterial swiss-army-knife pipeline for NGS data
Language: Python - Size: 25.3 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0
AhmedElsherbini/PADLOC_stats
Condense and summarize many results form PADLOC into CSV for heatmaps
Language: Python - Size: 72.3 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0
tseemann/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
Language: Perl - Size: 314 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 759 - Forks: 217
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Language: Python - Size: 61.3 MB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 395 - Forks: 42
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
Language: Python - Size: 27.3 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
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.
Language: R - Size: 9.77 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
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
Language: Python - Size: 9.77 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
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.
Language: R - Size: 10.7 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
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
Language: Shell - Size: 34.2 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0
gauravcodepro/KO-phylogenomics
python code which i coded using the mathematical expression for the genome based ontologies annotation and the phylogenomics informativeness
Language: Python - Size: 2.49 MB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0
gauravcodepro/miseq-nextseq-novaseq-genome
shell assembler that takes only the directory path and does all the cleaning of the reads, mapping, remapping and assembly. From start to finish everything by providing a simple directory path.
Language: Shell - Size: 27.3 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
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.
Language: Python - Size: 64.5 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
gauravcodepro/trinity-blast-machine-learning
a scalable and faster implementation for the genome and the transcriptome annotations for large scale sequencing datasets.
Language: Python - Size: 48.8 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
aglabx/OantigenMiner
Wonderful O-antigens Operons Finder
Language: Jupyter Notebook - Size: 17.9 MB - Last synced: 25 days ago - Pushed: 8 months ago - Stars: 1 - Forks: 0
liaoherui/StrainScan
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Language: Python - Size: 56.7 MB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 31 - Forks: 4
ClavelLab/genome-assembly
A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in the Clavel Lab
Language: Python - Size: 107 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
jordanlab/stringMLST
Fast k-mer based tool for multi locus sequence typing (MLST)
Language: Python - Size: 5.33 MB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 41 - Forks: 7
refresh-bio/PHIST
Phage-Host Interaction Search Tool
Language: C++ - Size: 9.98 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 24 - Forks: 1
paulstothard/cgview
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
Language: Java - Size: 471 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 36 - Forks: 15
paulstothard/cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
Language: Perl - Size: 693 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 27 - Forks: 17
BioinformaticsLabAtMUN/Promotech
Machine-learning-based general bacterial promoter prediction tool.
Language: C - Size: 89.3 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 37 - Forks: 10
adamd3/OrthoQuant
A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.
Language: Nextflow - Size: 30.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0
MaryAgopian/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 - Size: 55.7 KB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
esteinig/sketchy
Genomic neighbor typing of bacterial pathogens using MinHash :rat:
Language: Rust - Size: 20 MB - Last synced: 13 days ago - Pushed: over 1 year ago - Stars: 43 - Forks: 3
scbirlab/crispio
π± Designing CRISPRi experiments in bacteria
Language: Python - Size: 4.43 MB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
ipb-jianyang/eCIS-screen
This repository contains the code used for screening putative extracellular Contractile Injection System (eCIS) loci from genomic sequences.
Language: Perl - Size: 6.7 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 2
milnus/Magphi
Tool intended to pull out sequences and annotations between insertion sites specified by the user.
Language: Python - Size: 15.8 MB - Last synced: 13 days ago - Pushed: over 1 year ago - Stars: 12 - Forks: 3
Snitkin-Lab-Umich/prewas
R package to perform data pre-processing for more informative bacterial GWAS
Language: R - Size: 927 KB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 3
BU-ISCIII/taranis
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
Language: Python - Size: 3.95 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 5 - Forks: 3
xpolak37/COGtools
A computational tools for improving the functional annotation of bacterial genomes and the classification of CDSs into cllusters of orthologous groups (COGs). It allows summarizing annotations from different resources to provide a more accurate annotation of genes regarding their assignment into COGs and their categories.
Language: Python - Size: 6.99 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0
telatin/gan
π the Great Automatic Nomenclator β The Next Million Names for Archaea and Bacteria
Language: Python - Size: 8.82 MB - Last synced: 4 months ago - Pushed: almost 3 years ago - Stars: 29 - Forks: 5
henriksson-lab/btyper_website
An atlas of high-quality Bacillus cereus group genomes with standardized, manually curated metadata
Language: JavaScript - Size: 3.86 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
wennj/plasmid-collapse-gene-loss-unicycler-galaxy
Accompanying information to a scientific publication on the assembly of bacterial genomes using Illumina and nanopore sequencing data using Unicylcer.
Language: R - Size: 13.3 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
FemkeAhlers/Pneumococcal_PCR
Code for an upcoming paper on pneumococcal PCR-based diagnostics.
Language: R - Size: 92.8 KB - Last synced: 5 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
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 - Size: 2.39 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0
metageni/Scaffold_builder
Combining de novo and reference-guided assembly with Scaffold_builder
Language: Python - Size: 70.3 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 18 - Forks: 7
lmc297/BTyper
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
Size: 24.7 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1
charlesrocabert/Evo2Sim
Digital evolution model dedicated to bacterial in silico experimental evolution.
Language: C++ - Size: 7.52 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0
rbr7/Prog_in-Biological_and_Health_Science
Solutions for day-to-day computational problems in biological and health sciences.
Language: Python - Size: 25.4 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
jime-sg/deleat
DELEAT is a bioinformatic analysis pipeline for the design of large-scale genome deletions in bacterial genomes.
Language: Python - Size: 228 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 6 - Forks: 0
davidhwyllie/findNeighbour3
Bacterial relatedness server, supporting sequence clustering & mixture detection
Language: Python - Size: 53.6 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2
mb1511/GenomeWeb
Python package to create line drawings of genomic comparison 'webs'/'hive plots'
Language: Python - Size: 6.19 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0
GeeKboy2/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 - Size: 7.77 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 1
wanyuac/GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
Language: R - Size: 2.4 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 22 - Forks: 2
simonrharris/SKA
Split Kmer Analysis
Language: C++ - Size: 5.14 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 57 - Forks: 1
fatmakahveci/milestone
bacterial strain identification
Language: Python - Size: 8.78 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
mbhall88/thesis
My PhD thesis
Language: Jupyter Notebook - Size: 57 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0
koadman/libMems
a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches
Language: C++ - Size: 22.7 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
sablokgaurav/metapanran
MetaPanRan bring togthers Roary, PEPPAN, Pirate and PanROO for the comparative analysis of metagenomes and performs indepth analysis on evolutionary scales
Language: R - Size: 123 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0
rx32940/BactPrep
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
Language: Python - Size: 30.9 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 6 - Forks: 1
bohdandrahan/Genome-diversity-model-Seed-Root
π΅π΄π΅
Language: JavaScript - Size: 3.69 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
FemkeAhlers/Pneumococcal_LAMP
Code accompying an upcoming publication on the development of a pneumococcal LAMP assay.
Language: R - Size: 43 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
molevol-ub/BacterialDuplicates
Identification of putative duplicated genes among bacterial genomes
Language: Perl - Size: 2.22 MB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1
thyagoleal/mleprae-genomics_workflow
Snakemake workflow for processing Mycobacterium leprae whole genome sequencing data
Language: Python - Size: 99.6 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
BU-ISCIII/bacterial_wgs_training
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
Language: HTML - Size: 165 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 9 - Forks: 6
apredeus/10k_genomes
Various scripts for efficient processing of 10k Salmonella genomes
Language: Shell - Size: 42.1 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 12 - Forks: 2
lmc297/SNPBac
SNP and variant calling pipeline for bacteria
Size: 122 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 5 - Forks: 5
xx19941215/batch-shovill-assemblies
shovillζΉιζ§θ‘θζ¬ Batch Shovill can help you execute shovill batch assemblies.
Language: Go - Size: 6.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0
tseemann/noary
π£ π¦ A lightweight nucleotide bacterial ortholog clustering tool
Language: Perl - Size: 23.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 6 - Forks: 2
xx19941215/batch-prokka-assemblies
ProkkaζΉιζ§θ‘θζ¬ Batch Prokka can help you execute prokka batch assemblies.
Language: Go - Size: 3.61 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
niu-lab/gclust
genome sized sequences clustering
Language: C++ - Size: 27 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 12 - Forks: 3
Jtrachsel/pdtools
Functions for working with NCBI's Pathogen Detection data
Language: R - Size: 6.51 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0
bioinfoUQAM/Caribou
Alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning
Language: Python - Size: 9.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 1
mbhall88/mbhall88.github.io Fork of hydecorp/hydejack-starter-kit
The code behind my personal blog. Originally a fork of https://github.com/hydecorp/hydejack-starter-kit
Language: SCSS - Size: 1.33 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
xpolak37/the-COG-or
Package for improving the functional annotation of bacterial genomes, classification of protein-coding sequences into clusters of orthologous groups, and visualization of the final annotated genome.
Language: Python - Size: 2.69 MB - Last synced: 12 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
francesccoll/powerbacgwas
PowerBacGWAS: Power calculations for Bacterial GWAS
Language: Python - Size: 84.2 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0
uniqiqi/SamplePythonCodes
Two example R codes from the contributor. More systematic analysis codes will be available once the research paper is published.
Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
JRaviLab/dcia_evolution
Data and analysis for the DciA evolution manuscript | StallingsLab & JRaviLab
Language: R - Size: 128 MB - Last synced: 4 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
lmc297/BMiner
A companion application for analyzing and viewing BTyper output files in aggregate
Language: R - Size: 102 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1
AnikaKofodPetersen/Afili
The following is a bioinformatic workflow designed to find related phages and phage remnants. The workflow is not restricted to phages by any phage database.
Language: Python - Size: 520 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1
zhaoc1/nanoflow
Bioinformatics pipeline for nanopore sequencing data
Language: R - Size: 8.02 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 9 - Forks: 3
SheehabMuhammad/bacteria-analyzer
A Django Web Application for Bacteria Colony Count and Species Classification
Language: CSS - Size: 85.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
lmc297/seq2mlst
In silico multi-locus sequence typing (MLST) for bacterial genomes
Size: 353 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 5 - Forks: 3
crsl4/staph-visa
Reproducible scripts for the Su et al (2020) paper.
Size: 10.7 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
koadman/mauveAligner
command-line interface software for genome alignment
Language: C++ - Size: 61.6 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
andreas-wilm/nf-core-bacass Fork of nf-core/bacass
Simple bacterial assembly and annotation pipeline
Language: Nextflow - Size: 757 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0
tseemann/injecta
Insert genes into genomes to aid synthetic test data generation
Language: Perl - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0
hcdenbakker/mcOutbryk
SNP calling pipeline using mccortex
Language: Python - Size: 52.7 KB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 1
