HiFi DeepVariant + WhatsHap workflowHiFi DeepVariant + WhatsHap workflow

Overview

HiFi DeepVariant + WhatsHap workflow

Workflow steps

  1. align HiFi reads to reference with pbmm2
  2. call small variants with DeepVariant, using two-pass method (DeepVariant ➡️ WhatsHap phase ➡️ WhatsHap haplotag ➡️ DeepVariant)
  3. phase small variants with WhatsHap
  4. haplotag aligned BAMs with WhatsHap and merge

Directory structure within basedir

.
├── cluster_logs  # slurm stderr/stdout logs
├── reference
│   ├── reference.chr_lengths.txt  # cut -f1,2 reference.fasta > reference.chr_lengths.txt
│   ├── reference.fasta
│   └── reference.fasta.fai
├── samples
│   └── 
   
      # sample_id regex: r'[A-Za-z0-9_-]+'
│       ├── whatshap/  # phased small variants; merged haplotagged alignments
│       ├── logs/  # per-rule stdout/stderr logs
│       ├── aligned/  # intermediate
│       ├── deepvariant/  # intermediate
│       ├── deepvariant_intermediate/  # intermediate
│       └── whatshap_intermediate/  # intermediate
├── smrtcells
│   ├── done  # move folders from smrtcells/ready to smrtcells/done to prevent re-processing
│   └── ready
│       └── 
    
       # uBAMs or FASTQs per sample
│                        # filename regex: r'm\d{5}[Ue]?_\d{6}_\d{6}).(ccs|hifi_reads).bam' or r'm\d{5}[Ue]?_\d{6}_\d{6}).fastq.gz'
└── workflow  # clone of this repo

    
   

To run the pipeline

$ conda create \
    --channel bioconda \
    --channel conda-forge \
    --prefix ./conda_env \
    python=3 snakemake mamba lockfile

$ conda activate ./conda_env

$ sbatch workflow/run_snakemake.sh <sample_id>
Owner
William Rowell
Geneticist & 1x programmer on a good day. BFX applications @PacificBiosciences.
William Rowell
HiFi-GAN: High Fidelity Denoising and Dereverberation Based on Speech Deep Features in Adversarial Networks

HiFiGAN Denoiser This is a Unofficial Pytorch implementation of the paper HiFi-GAN: High Fidelity Denoising and Dereverberation Based on Speech Deep F

Rishikesh (ऋषिकेश) 79 Nov 26, 2021
HiFi-GAN: Generative Adversarial Networks for Efficient and High Fidelity Speech Synthesis

HiFi-GAN: Generative Adversarial Networks for Efficient and High Fidelity Speech Synthesis Jungil Kong, Jaehyeon Kim, Jaekyoung Bae In our paper, we p

Rishikesh (ऋषिकेश) 22 Dec 1, 2021
Implementation of TTS with combination of Tacotron2 and HiFi-GAN

Tacotron2-HiFiGAN-master Implementation of TTS with combination of Tacotron2 and HiFi-GAN for Mandarin TTS. Inference In order to inference, we need t

SunLu Z 3 Nov 29, 2021
Combine Tacotron2 and Hifi GAN to generate speech from text

EndToEndTextToSpeech Combine Tacotron2 and Hifi GAN to generate speech from text Download weights Hifi GAN -> hifi_gan/checkpoint/ : pretrain 2.5M ste

Phạm Quốc Huy 1 Nov 27, 2021
Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

Luigi is a Python (3.6, 3.7 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow managemen

Spotify 15.2k Dec 3, 2021
A powerful workflow engine implemented in pure Python

Spiff Workflow Summary Spiff Workflow is a workflow engine implemented in pure Python. It is based on the excellent work of the Workflow Patterns init

Samuel 1.1k Nov 23, 2021
Unified Interface for Constructing and Managing Workflows on different workflow engines, such as Argo Workflows, Tekton Pipelines, and Apache Airflow.

Couler What is Couler? Couler aims to provide a unified interface for constructing and managing workflows on different workflow engines, such as Argo

Couler Project 616 Dec 1, 2021
Reusable workflow library for Django

django-viewflow Viewflow is a lightweight reusable workflow library that helps to organize people collaboration business logic in django applications.

Viewflow 2.1k Dec 1, 2021
Python Development Workflow for Humans.

Pipenv: Python Development Workflow for Humans [ ~ Dependency Scanning by PyUp.io ~ ] Pipenv is a tool that aims to bring the best of all packaging wo

Python Packaging Authority 22.5k Nov 29, 2021
An audio digital processing toolbox based on a workflow/pipeline principle

AudioTK Audio ToolKit is a set of audio filters. It helps assembling workflows for specific audio processing workloads. The audio workflow is split in

Matthieu Brucher 233 Nov 1, 2021
PyWorkflow(PyWF) - A Python Binding of C++ Workflow

PyWorkflow(PyWF) - A Python Binding of C++ Workflow 概览 C++ Workflow是一个高性能的异步引擎,本项目着力于实现一个Python版的Workflow,让Python用户也能享受Workflow带来的绝佳体验。

Sogou-inc 65 Nov 8, 2021
Git Plan - a better workflow for git

git plan A better workflow for git. Git plan inverts the git workflow so that you can write your commit message first, before you start writing code.

Rory Byrne 165 Nov 9, 2021
Python Development Workflow for Humans.

Pipenv: Python Development Workflow for Humans [ ~ Dependency Scanning by PyUp.io ~ ] Pipenv is a tool that aims to bring the best of all packaging wo

Python Packaging Authority 22.5k Dec 3, 2021
Make tree planting a part of your daily workflow. 🌳

Continuous Reforestation Make tree planting a part of your daily workflow. ?? A GitHub Action for planting trees within your development workflow usin

protontypes 157 Nov 18, 2021
This repository contains free labs for setting up an entire workflow and DevOps environment from a real-world perspective in AWS

DevOps-The-Hard-Way-AWS This tutorial contains a full, real-world solution for setting up an environment that is using DevOps technologies and practic

Mike Levan 399 Dec 2, 2021
LOC-FLOW is an “hands-free” earthquake location workflow to process continuous seismic records

LOC-FLOW is an “hands-free” earthquake location workflow to process continuous seismic records: from raw waveforms to well located earthquakes with magnitude calculations. The package assembles several popular routines for sequential earthquake location refinements, suitable for catalog building ranging from local to regional scales.

Miao Zhang 33 Nov 28, 2021
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

Germline Mutation Calling This Snakemake workflow follows the GATK best-practice recommandations to call small germline variants. The pipeline require

null 6 Oct 2, 2021
A frontend to ease the use of pulseaudio's routing capabilities, mimicking voicemeeter's workflow

Pulsemeeter A frontend to ease the use of pulseaudio's routing capabilities, mimicking voicemeeter's workflow Features Create virtual inputs and outpu

Gabriel Carneiro 25 Nov 25, 2021
A project based example of Data pipelines, ML workflow management, API endpoints and Monitoring.

MLOps template with examples for Data pipelines, ML workflow management, API development and Monitoring.

Utsav 18 Nov 25, 2021
Teaching end to end workflow of deep learning

Deep-Education This repository is now available for public use for teaching end to end workflow of deep learning. This implies that learners/researche

Data Lab at College of William and Mary 1 Oct 21, 2021
A python based app to improve your presentation workflow

Presentation Remote A remote made for making presentations easier by enabling all the members to have access to change the slide and control the flow

Parnav 1 Oct 28, 2021
A Snakemake workflow for standardised sc/snRNAseq analysis

single_snake_sequencing - sc/snRNAseq Snakemake Workflow A Snakemake workflow for standardised sc/snRNAseq analysis. Every single cell analysis is sli

IMS Bio2Core Facility 1 Nov 2, 2021
redun aims to be a more expressive and efficient workflow framework

redun yet another redundant workflow engine redun aims to be a more expressive and efficient workflow framework, built on top of the popular Python pr

insitro 245 Nov 21, 2021
SaltConf21: Adding Workflow Approval to Salt

SaltConf21: Adding Workflow Approval to Salt Running To run the example, install Docker and docker-compose and run the following commands: docker-comp

SSYS Sistemas 4 Nov 24, 2021
A workflow management tool for numerical models on the NCI computing systems

Payu Payu is a climate model workflow management tool for supercomputing environments. Payu is currently only configured for use on computing clusters

The Payu Organization 10 Nov 18, 2021
A basic animation modding workflow for FFXIV

AnimAssist Provides a quick and easy way to mod animations in FFXIV. You will need: Before anything, the VC++2012 32-bit Redist from here. Havok will

liam 16 Nov 24, 2021
ClearML - Auto-Magical Suite of tools to streamline your ML workflow. Experiment Manager, MLOps and Data-Management

ClearML - Auto-Magical Suite of tools to streamline your ML workflow Experiment Manager, MLOps and Data-Management ClearML Formerly known as Allegro T

ClearML 2.8k Dec 3, 2021
DALLE-tools provided useful dataset utilities to improve you workflow with WebDatasets.

DALLE tools DALLE-tools is a github repository with useful tools to categorize, annotate or check the sanity of your datasets. Installation Just clone

null 2 Dec 1, 2021