Tutorials and Demos

Real-World Demos and Benchmarks

This page contains detailed real-world test workflows and performance benchmarks across various plant organellar datasets.

Demo 1: Arabidopsis thaliana (HiFi data)

Dataset download link: Arabidopsis thaliana (550Mb)

Step 1: Download dataset

wget https://github.com/bichangwei/PMAT/releases/download/v1.1.0/Arabidopsis_thaliana_550Mb.fa.gz

Step 2: One-step assembly with autoMito

PMAT autoMito -i Arabidopsis_thaliana_550Mb.fa.gz -o ./test1 -t hifi -m

Step 3: Manual extension with graphBuild (if autoMito requires customization)

PMAT graphBuild -i ./test1/subsample/ -a ./test1/assembly_result/ -o ./test1_gfa -s 1 2 3 -d 5

Assessment output (PMAT_orgAss.txt)

 ==========================================================
             Mitochondrial Assembly Assessment             
 ==========================================================

 Basic Statistics:
 ----------------------------------------------------------
 Total contigs:          16  
 Total length:           367.8 kb
 Average depth:          28.4 x
 Total genes found:      24/24 (100.0%)
 Duplicated contigs:     3   

 Per-contig Details:
 ----------------------------------------------------------
 Contig ID   Genes     Gene List           
 ----------------------------------------------------------
 300         4         atp1,cox1,nad1,nad2 
 2150        1         atp6                
 908         4         atp9,ccmB,cox2,nad9 
 1221        2         atp4,nad4L          
 729         4         ccmC,ccmFn,cox3,nad3
 727         1         nad3                
 1524        1         atp9                
 2150        1         atp6                
 749         6         atp8,matR,mttB,na...
 298         3         ccmFc,cob,nad6      
 ----------------------------------------------------------

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Demo 2: Malus domestica (HiFi data)

Dataset download link: Malus domestica (540Mb)

Step 1: Download dataset

wget https://github.com/bichangwei/PMAT/releases/download/v1.1.0/Malus_domestica.540Mb.fasta.gz

Step 2: Run assembly

PMAT autoMito -i Malus_domestica.540Mb.fasta.gz -o ./test2 -t hifi -m

Assessment output (PMAT_orgAss.txt)

 ==========================================================
             Mitochondrial Assembly Assessment             
 ==========================================================

 Basic Statistics:
 ----------------------------------------------------------
 Total contigs:          4   
 Total length:           397.0 kb
 Average depth:          31.1 x
 Total genes found:      24/24 (100.0%)
 Duplicated contigs:     1   

 Per-contig Details:
 ----------------------------------------------------------
 Contig ID   Genes     Gene List           
 ----------------------------------------------------------
 1           20        atp1,atp4,atp8,at...
 2           6         atp6,atp9,matR,na...
 ----------------------------------------------------------

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Demo 3: Phaseolus vulgaris (CLR data)

Step 1: Download tested CLR data using IBM Aspera

ascp -v -QT -l 400m -P33001 -k1 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR291/006/SRR2912756/SRR2912756_subreads.fastq.gz .

Step 2: Run autoMito with NextDenovo error correction

PMAT autoMito -i SRR2912756_subreads.fastq.gz -o ./test_clr -t clr -N path/to/nextDenovo -m

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Demo 4: Populus deltoides (ONT data)

Step 1: Download tested ONT data using IBM Aspera

ascp -v -QT -l 400m -P33001 -k1 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR122/038/SRR12202038/SRR12202038_1.fastq.gz .

Step 2: Run autoMito with Canu error correction

PMAT autoMito -i SRR12202038_1.fastq.gz -o ./test_ont -t ont -S canu -C path/to/canu -m

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Benchmark Performance Table

Dataset	Data Size	Threads & Memory Options	Run Time	Organellar Coverage
Arabidopsis thaliana	550Mb	-T 50	6m27s	4x
Arabidopsis thaliana	550Mb	-T 50 -m	6m38s	4x
Malus domestica	540Mb	-T 50	7m38s	<1x
Malus domestica	540Mb	-T 50 -m	7m19s	<1x
Juncus effusus	216Mb	-T 50	4m56s	<1x
Juncus effusus	216Mb	-T 50 -m	4m48s	<1x