NOVOPlasty

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NOVOPlasty ran successfully but did not generate a contig

5

Hello, how are you? I'm currently running NOVOPlasty for two fish species, and while there haven't been any errors reported, I've encountered an issue. The Circularized_assembly_1_zfish.fasta file appears to be...

laribritto

The genome has been circularized, but 2 different contigs

5

I am assembling turtles mitogenomes and in some cases the output I obtain is a "Circularized genome", actually made up of 2 non overlapping contigs: in all these cases, the...

LiviaT93

Building Hash Table...Killed

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Hello I got this message "Building Hash Table...Killed" when I try to assembly animal mitogenome. What does it mean? Running with test dataset was worked well Thank you very much

Ekgachai

In the Heteroplasmy vcf files reporting the heteroplasmic positions, the DP is reporting the "raw depth": does it mean the number of reads supporting that variant, or the number of...

LiviaT93

Visualization with Circos

1

Hi, to generate the Circos visualization for fish mitochondrial DNA, you have to manually update the annotation file. Is it possible to use the annotations from the MitoFish annotator? https://github.com/ndierckx/NOVOPlasty/blob/master/Circos/Circos_human_anno2.txt

laribritto

Minimum header requirements to be accepted as input?

2

Hello! I'm trying to assemble the mitogenome for sequence data that has the following header format which seems to have been edited, any idea if I can modify it so...

lightworms

Input data metrics explanation, % of mtDNA reads of the total sequence reads that mapped to the whole mtDNA_follow up

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Dear Nicolas, Just a follow up question for the issue #216 How do I know the right % of mtDNA reads of the total sequence reads that mapped to the...

AliBasuony2022

substr outside of string

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Hello, I cannot perform an heteroplasmy analysis because I get the error "at NOVOPlasty4.3.3.pl line 11411". Is there a way to avoid getting this error message? Best reagards.

olepais

Input File Format

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[config_palmetto.txt](https://github.com/ndierckx/NOVOPlasty/files/14101154/config_palmetto.txt) Hello, I keep getting the Input file error. I've gone through other's issues but can't seem to find one that matches on input (maybe I missed it though). I...

tetrahedraldogwood

The two input files are identical, please check the configuration file!

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i have used the test data for novoplasty running, and it showed my input files are identical, but my input is different.please .Would you please help me answer it.my config.txt...

qiguaidedashan