Analysis pipeline for the GUIDE-seq assay.

CAST-Seq Bioinformatic pipeline

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

🐴 CLinically Okay Metagenomic Pipeline 🐴

Protein structure comparison tools such as SSAP and SNAP

NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes

A toolbox for comparative genomics.

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Structural variant VCF annotation, duplicate removal and comparison

Statistical Analysis of Metagenomic Profiles

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Collect of SO Ontologies

🌈 Interactive analysis of metagenomics data

UW Virology's Clinically OK Metagenomic Pipeline

Interactive roadmaps, guides and other educational content to help developers grow in their careers.

Chromosome-level scaffolding using multiple references

Snakemake pipeline using CD-HIT-OTU-MiSeq utilities to extract OTUs from paired-end reads

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

Fast and flexible ORF finder

Protein Graph Library

a template that resembles the word template provided the grad college of uiowa

Visualizer for pandas data structures

Antibiotic resistance prediction in minutes

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Reproducible Evaluation of Gene-Level Metagenomics Tools

General Comments about Open Source Antibiotics Research