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ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

augustus

Genome annotation with AUGUSTUS

barque

Environmental DNA metabarcoding taxonomic identification

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

bioinfokit

Bioinformatics data analysis and visualization toolkit

bioinformatica2019

Bitácoras y archivos

bioinformatica_anotacion2019

Curso "Secuenciación masiva y anotación de genes" UAM-Iztapalaoa

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

co1classifier

This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

concordia_workshop_biopython

Pratical to learn basic Biopython usage

decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

deeprotgo

exp2go

exp2GO is a novel method for the computational prediction of gene function annotations

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

github

goatools

Python scripts to find enrichment of GO terms

hmmer2go

Annotate DNA sequences for Gene Ontology terms

imputationserver-docker

Docker Image for Michigan Imputation Server

lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

metagenomics

🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean

metator

Metagenomic binning based on Hi-C data

metaworks

MetaWorks is a flexible multi-marker metabarcode pipeline for processing paired-end Illumina reads from raw fastq.gz files to taxonomic assignments.

microbiomehd

Cross-disease comparison of case-control gut microbiome studies

mitophast

mumuki-proyecto-base

nanodj

NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly

neurogap_downsampling

novoplasty

NOVOPlasty - The organelle assembler and heteroplasmy caller