Stars
Collection of bioinformatics training materials
Regularly used bioinformatics script for different purposes
A pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes.
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
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A pipeline for running SNP-based phylogenetic analysis
Ultimate list of Linux bash commands, cheatsheets and resources
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Collection of bioinformatics training materials
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
LANL-Bioinformatics / PhaME
Forked from sanahmed/PhaMEGiven a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (gene…
Chromosome-level scaffolding using multiple references
A pipeline to generate a phylogenetic tree from huge SNP data
Building a fully automized pipeline for phylogenomic analyses based on the BUSCO toolkit
Making whole bacterial genome sequencing data analysis easy
A scalable bacterial genome assembly, annotation and analysis pipeline
MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates