Mandalorion is a pipeline to identify isoforms from full-length cDNA sequencing data.

It takes R2C2/C3POa and/or PacBio/ccs/lima data and defines high confidence isoform consensus sequences and alignments. You can mix and match R2C2/PacBio reads and fasta/fastq files (quality scores are ignored). Mandalorion is not tested for use with regular ONT reads.

References:

• Volden, R., Schimke, K.D., Byrne, A. et al. Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion. Genome Biol 24, 167 (2023).

• Mandalorion on GitHub

This application requires a graphical connection using NX

• Module Name: mandalorion (see the modules page for more information)
• Set the number of alignment threads with -t/--minimap2_threads. Default at the time of writing is 8.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task 6
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mandalorion

[user@cn3144 ~]$ Mando.py -p ./ -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa -f input.fa -t $SLURM_CPUS_PER_TASK

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mandalorion.sh). For example:

#!/bin/bash
set -e
module load mandalorion

Mando.py \
  -p ./ \
  -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf \
  -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa \
  -f input.fa \
  -t $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=# [--mem=#] mandalorion.sh

Create a swarmfile (e.g. mandalorion.swarm). For example:

Mando.py -f input1.fa -p sample1 -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa -t $SLURM_CPUS_PER_TASK
Mando.py -f input2.fa -p sample2 -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa -t $SLURM_CPUS_PER_TASK
Mando.py -f input3.fa -p sample3 -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa -t $SLURM_CPUS_PER_TASK
Mando.py -f input4.fa -p sample4 -g /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode/genes.gtf -G /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa -t $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f mandalorion.swarm [-g #] [-t #] --module mandalorion