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STRAIN RESOLUTION OF ASSEMBLIES USING STRAINBERRY: TAPIR Pipeline version 1.0dev
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The typical command for running the pipeline is as follows:
nextflow run main.nf --reads "PathToReadFile(s)" --output_dir "PathToOutputDir" --assemblies "PathToAssemblies"
Mandatory arguments:
--reads Query fastqz file of sequences you wish to supply as input (e.g., "/MIGE/01_DATA/01_FASTQ/T055-8-*.fastq.gz")
--output_dir Output directory (e.g., "/MIGE/01_DATA/03_ASSEMBLY")
--assemblies must be Flye assembly (e.g., "/MIGE/01_DATA/03_ASSEMBLY/*_FLYE/T055-8-*.fasta")
Optional arguments:
--help This usage statement.
--version Version statement
This pipeline attempts to resolve strains from long-read assemblies. This Nextflow pipeline was adapted from the original author's Github page.
An example of a command to run this pipeline is:
nextflow run main.nf --reads "Sample_files/*.fastq.gz" --output_dir "test2" --assemblies "*.fasta"
To extract strain-resolved genomes from the assemblies and generate other useful statistics report, kindly follow the steps outlined here.
This is an ongoing project at the Microbial Genome Analysis Group, Institute for Infection Prevention and Hospital Epidemiology, Üniversitätsklinikum, Freiburg. The project is funded by BMBF, Germany, and is led by Dr. Sandra Reuter.
The TAPIR (Track Acquisition of Pathogens In Real-time) team.
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