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Hi,
I have assembled the mitogenomes of 8 Microctonus aethiopoides using Flye in meta mode on ONT data. The mitogenomes were extracted from the assembly using the GetOrganelle tool. According to the …
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Hi, I want to use GetOrganelle to assemble plant mitochondria genome and meet a problem. Here is my log file and result files:
[assemble_plant_mitochondria.zip](https://github.com/Kinggerm/GetOrga…
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Hi Developers!!
Thanks for making such a straightforward tool for simulation. I wish to simulate reads from Mitochondrial genome reference fasta but I am confused about what distribution should I c…
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Hi,
Firstly, I want to thank you for this amazing tool! I've been using it consistently during my PhD, and it has been immensely helpful!
I have a few questions about the circularization check…
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When I assemble PacBio HiFi reads of a Eukaryotic linear genome through HiFiasm, I get a couple of circular contigs. The linear contigs are appended with an `l` in the fasta header, and the circular c…
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I'm using doFasta -2 to extract the consensus sequence from bwa alignment (bam) files (for mitochondrial genomes). I've found that if there is a variable length repeat, ANGSD always generates the long…
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Hi,
I am trying to assemble three plant mitochondrial genome sequences using Novoplasty. I successfully assembled two mitochondrial genomes. But When I try to assemble the third genome sequence usi…
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Dear Changwei,
I was using autoMito to generate the 2 gfa files (raw and master) of the assembled Malus Domestica genome (as in Demo2) with the code as follows:
~/PMAT-1.5.3/bin/PMAT autoMito -i…
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Some genomes exhibit very strong biases in their mutations between their reference and anti-reference bases. For example, human mitochondrial DNA shows a 4X higher mutation frequency for reference G->…
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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkag…