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Pipeface
Overview
Pipefaceee.
Nextflow pipeline to process long read ONT and/or pacbio HiFi data.
Pipeface's future hold's mitochondrial, STR, CNV and tandem repeat calling.
Workflow
Singleton
%%{init: {'theme':'dark'}}%%
flowchart LR
input_data("Input data: ONT fastq.gz and/or ONT fastq and/or ONT uBAM and/or pacbio HiFi uBAM")
merging{{"Merge runs (if needed)"}}
alignment{{"bam to fastq conversion (if needed), alignment,
...
Type: Nextflow
Creators: Leah Kemp, Andre Reis, Ira Deveson, Kisaru Liyanage, Matthew Downton, Hardip Patel, Kirat Alreja, This is a highly collaborative project, with many contributions from the Genomic Technologies Lab. Notably, Dr Andre Reis and Dr Ira Deveson are closely involved in the development of this pipeline. Optimisations involving DeepVariant and DeepTrio have been contributed by Dr Kisaru Liyanage and Dr Matthew Downton from the National Computational Infrastructure, with support from Australian BioCommons as part of the Workflow Commons project. Haploid-aware mode has been contributed by Dr Hardip Patel & Kirat Alreja from the National Centre for Indigenous Genomics. The installation and hosting of software used in this pipeline has and continues to be supported by the Australian BioCommons Tools and Workflows project (if89).
Submitter: Leah Kemp
Nextflow Pipeline for DeepVariant
This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.
Quickstart Guide
- Edit the
pipeline_params.ymlfile to include:
samples: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to''if not required), and the model type.ref: path to the reference FASTA (ensure ...
