plant mitochondria genome

[fengyuanli304]

Dear Dr. Jin, I tried to assemble one plant mitochondria genome and started using the following settings. 1, get_organelle_from_reads.py -1 f3_R1_clean.fastq.gz -2 f3_R2_clean.fastq.gz -o mitochondria_output -R 50 -k 21,45,65,85,105 -P 1000000 -F embplant_mt -s species_from_same_genus.fasta -t 16

The graph has contigs that have extremely high coverage, so I increase the maximum kmer value and rerun the same dataset using the following settings. 2, get_organelle_from_reads.py -1 f3_R1_clean.fastq.gz -2 f3_R2_clean.fastq.gz -o mitochondria_output3 -R 80 -k 45,65,85,105,127 -P 1000000 -F embplant_mt -s species_from_same_genus.fasta -t 16

2.get_org.log.txt I manually remove non-target contigs from embplant_pt and then do the completion using get_organelle_from_assembly.py.

But Disentangling failed: 'Free variable > 10 is not accepted yet!' What should I do with these results? Waiting for your reply.

Sincerely.

[Kinggerm]

Unfortunately, there is barely hope for achieving a complete mitogenome with current Illumina data. According to the graph, there are many cp->mt transfers and many repeats that Illumina data cannot solve.

The only good thing is that the assembly graph of pt+mt seems complete, so that if you are doing a phylogenetic study, you many extract all the mt genes from the post-manual-completion contigs.

[fengyuanli304]

Dear Dr. Jin,

Big thanks for your reply. I have Nanopore sequencing data. what should I do to improve this result?

Best

[Kinggerm]

1. Clean the graph to achieve a pt+mt complete graph with both pt and mt contigs. Remove the up-left short-repeat contigs, I believe those are not organelle contigs.
2. Map Nanopore sequencing data to the cleaned graph using GraphAligner.
3. Using Traversome to estimate and extract all organelle components. Traversome is a tool under development, but I expect both pt and mt can be isolated.

Please let me know your updates.

[liuchanglai]

can you describe in detail the following operation?

1. Clean the graph to achieve a pt+mt complete graph with both pt and mt contigs. Remove the up-left short-repeat contigs, I believe those are not organelle contigs.

[Kinggerm]

can you describe in detail the following operation?

1. Clean the graph to achieve a pt+mt complete graph with both pt and mt contigs. Remove the up-left short-repeat contigs, I believe those are not organelle contigs.

a) Load the graph in Bandage. b) Pick those non-target contigs, then click on Edit -> Remove selection from graph. c) Click on Output -> Save visible graph to GFA.

Please read the GetOrganelle paper to understand the principles for identification of non-target contigs.