hasindu2008/nci-scripts

PBS scripts for running nanopore genomics analyses on NCI Gadi

nci-scripts

Example PBS scripts for running long read genomics analyses on Australia's NCI Gadi Supercomputer.

These scripts use software installed under the if89 project (Australian BioCommons Tools and Workflows project). With your NCI account, simply join the if89 project using the myNCI and start using these scripts with software already installed on Gadi through project if89.

See the comments in the scripts to identify which variables you should change. These scripts are intentionally kept minimal as they are intended to serve as examples for you to quickly get started.

Read Alignment

• align/minimap2-samtools.pbs.sh - Align a FASTQ file to a reference using Minimap2 and sort using samtools to create a BAM file (and the BAM index).

Assembly

• asm/hifiasm.pbs.sh - assemble a genome using hifiasm
• asm/quast.pbs.sh - evaluate a assembly using quast

S/BLOW5 Basecalling

• basecall/buttery-eel-guppy.pbs.sh - Basecall a S/BLOW5 file using buttery-eel wrapper for Guppy.
• basecall/buttery-eel-dorado.pbs.sh - Basecall a S/BLOW5 file using buttery-eel wrapper for Dorado.
• basecall/slow5-dorado.pbs.sh - Basecall a S/BLOW5 file using slow5-dorado, a fork of ONT's Dorado that supports S/BLOW5.

S/BLOW5 Modification calling

• modcall/f5c-call-methylation.pbs.sh - Perform methylation calling of a S/BLOW5 file using f5c, a GPU accelerated version of nanopolish. You must execute f5c-index.pbs.sh under the preparation section first.
• modcall/buttery-eel-guppy.pbs.sh - Modification calling of a S/BLOW5 file using buttery-eel wrapper for Guppy.
• modcall/buttery-eel-dorado.pbs.sh - Modification calling of a S/BLOW5 file using buttery-eel wrapper for Dorado.

Preparation

• prep/f5c-index.pbs.sh - Perform f5c index (required before running f5c call-methylation or eventalign).
• prep/pod5-to-merged-blow5.pbs.sh - Converts a POD5 data set to a single merged BLOW5 file using blue-crab and slow5tools

Data Transfer

• transfer/s3-download.pbs.sh - Download an example BLOW5 file and an index from an S3 bucket using aws cli.