Name: NGI-NeutronStar
Owner: Science For Life Laboratory
Description: De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.
Forked from: remiolsen/NGI-NeutronStar
Created: 2017-12-07 09:01:56.0
Updated: 2018-01-11 19:31:15.0
Pushed: 2017-12-11 16:31:11.0
Size: 1855
Language: Groovy
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NGI-NeutronStar is a bioinformatics best-practice analysis pipeline used for de-novo assembly and quality-control of 10x Genomics Chromium data. It's developed and used at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
It is recommended that you start the pipeline inside a unix screen (or alternatively tmux).
To assemble a single sample, the pipeline can be started using the following command:
flow run -profile nextflow_profile /path/to/NGI-NeutronStar/main.nf [Supernova options] (--clusterOptions)
nextflow_profile is one of the environments that are defined in the file nextflow.config[Supernova options] are the following options that are following supernova options (use the command supernova run --help for a more detailed description or alternatively read the documentation available by 10X Genomics)--fastqs required--id required--sample--lanes--indices--bcfrac--maxreads--clusterOptions are the options to feed to the HPC job manager. For instance for SLURM --clusterOptions="-A project -C node-type"--genomesize required The estimated size of the genome(s) to be assembled. This is mainly used by Quast to compute NGxx statstics, e.g. N50 statistics bound by this value and not the assembly size.NGI-NeutronStar also supports adding the above parameters in a .yaml file. This way you can run several assemblies in parallel. The following example file (sample_config.yaml) will run two assemblies of the test data included in the Supernova installation, one using the default parameters, and one using barcode downsampling:
mesize: 1000000
les:
id: testrun
fastqs: /sw/apps/bioinfo/Chromium/supernova/1.1.4/assembly-tiny-fastq/1.0.0/
id: testrun_bc05
fastqs: /sw/apps/bioinfo/Chromium/supernova/1.1.4/assembly-tiny-fastq/1.0.0/
maxreads: 500000000
bcfrac: 0.5
Run nextflow using nextflow run -profile -params-file sample_config.yaml /path/to/NGI-NeutronStar/main.nf (--clusterOptions)
These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. Written by Remi-Andre Olsen (@remiolsen).
