Julien A Nguinkal's Projects
Ce repo est créé pour partager toutes les ressouces des vidéos du challenge 30DaysGenerativeAI sur la chaîne Youtube LeCoinStat
Another Gtf/Gff Analysis Toolkit
A Nextflow pipeline for NGS antimicrobial resistance profiling. From raw NGS FASTQ to rendered AMR profiles
Antimicrobial Resistance Analysis
Antimicrobial Resistance Identification By Assembly
AUGUSTUS v3.2.1 for installation on Mac OS X
A flexible pipeline for complete analysis of bacterial genomes
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Introduction to Bash for bioinformatics
Config files for my GitHub profile.
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
Conda recipes for the bioconda channel.
Interactive quality assessment of genome assemblies
Nextstrain Analysis Automation Script. This wrapper Python script is developed to automate the analysis steps of RNA virus sequences as much as possible using Nextstrain.
Pipelines, code and ressources for creating a fully haplotype-resolved T2T assembly of the African catfish (Clarias gariepinus) combining PacBio HiFi, ONT long reads and Hi-C data.
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs
Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.
Data and resources accompanying the manuscript on Pathogen Next-Generation Sequencing in the East African Community. Includes NPHL survey responses and metadata on bacterial pathogens
Accessing NCBI’s Entrez databases using EDirect utility
convert various features into a GFF-like file for use in genome browsers
Unix, R and python tools for genomics and data science
gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.
:zap: Dynamically generated stats for your github readmes
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
An accurate GFF3/GTF lift over pipeline
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies