Workflows
What is a Workflow?Filters
From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere
Functional annotation of protein sequences
Structural and functional genome annotation with Funannotate
Masking repeats in a genome using RepeatMasker
Assemble long reads with Flye, then view assembly statistics and assembly graph
EBP-Nor Genome Assembly pipeline
This repository contains the EBP-Nor genome assembly pipeline. This pipeline is implemented in snakemake. This pipeline is developed to create haplotype-resolved genome assemblies from PacBio HiFi reads and HiC reads, and is primarly designed for diploid eukaryotic organisms. The pipeline is designed to work on a linux cluster with slurm as workload manager.
Requirements & Setup
Some software need to be configured/installed before the pipeline can be run ...
CLAWS (CNAG's Long-read Assembly Workflow in Snakemake)
Snakemake Pipeline used for de novo genome assembly @CNAG. It has been developed for Snakemake v6.0.5.
It accepts Oxford Nanopore Technologies (ONT) reads, PacBio HFi reads, illumina paired-end data, illumina 10X data and Hi-C reads. It does the preprocessing of the reads, assembly, polishing, purge_dups, scaffodling and different evaluation steps. By default it will preprocess the reads, run Flye + Hypo + purge_dups + yahs and evaluate ...
Type: Snakemake
Creators: Jessica Gomez-Garrido, Fernando Cruz (CNAG), Francisco Camara (CNAG), Tyler Alioto (CNAG)
Submitter: Jessica Gomez-Garrido
Welcome to the pipesnake. Let's get started.
Introduction
pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity ...