barrantesisrael

repromicrobiome2021

any2fasta

Convert various sequence formats to FASTA

awesome

:sunglasses: Curated list of awesome lists

awesome-R

A curated list of awesome R packages, frameworks and software.

barrantesisrael.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

canu

A single molecule sequence assembler for genomes large and small.

Dual_RNAseq_Hsapiens_Spyogenes_IAV

Dual_RNAseq_review_analysis

mbt.microbiome.2021

Scripts and tutorials for the analysis of microbiome data (UMR MBT Praktikum)

gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

isb_course_2023

Materials and presentation for the 2023 ISB Microbiome course.

kraken

Kraken taxonomic sequence classification system

mbtmicrobiome2023

MegaGO

Calculate semantic distance for sets of Gene Ontology terms

MicroArray_Affymetrix_Analysis

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

neptune

Neptune: Genomic Signature Discovery

oneliners

Useful bash one-liners for bioinformatics.

panito

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment

piggy

Pipeline for analysing intergenic regions in bacteria

pnew202401

Roary

Rapid large-scale prokaryote pan genome analysis

Scoary

Pan-genome wide association studies

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

starter-academic

test.github.io

README

Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

umr.praktikum

Repository of scripts and tutorials for analyzing microbiome data (UMR Praktikum 2020).