Alternatives and similar repositories for pathogen-informatics-training

Users that are interested in pathogen-informatics-training are comparing it to the libraries listed below

• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆83Updated 7 years ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆109Updated 4 months ago
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆121Updated last year
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆140Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated last year
• AstrobioMike / bit
  Bioinformatics Tools
  ☆89Updated this week
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆104Updated 6 months ago
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆140Updated last month
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆94Updated 5 years ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆118Updated 2 months ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆141Updated last year
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆92Updated last year
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆77Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆126Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆93Updated last week
• CompSynBioLab-KoreaUniv / FunGAP
  FunGAP: fungal Genome Annotation Pipeline
  ☆111Updated 2 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆111Updated 9 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆63Updated 11 months ago
• waldronlab / curatedMetagenomicData
  Curated Metagenomic Data of the Human Microbiome
  ☆139Updated last month
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆47Updated 5 years ago
• sunbeam-labs / sunbeam
  A robust, extensible metagenomics pipeline
  ☆174Updated last week
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆44Updated 3 years ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• husonlab / megan-ce
  MEGAN Community Edition
  ☆73Updated last year
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆75Updated last year
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆174Updated 3 months ago