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KmerGenie estimates the high-quality k-mer period for genome de novo assembly." More info are at KmerGenie -
The computer analysis of APOL1 and single nucleotide polymorphisms in chronic kidney disease (CDK). Any help anyone can provide me with will be really appreciated. Thank you very much, everyoneLeave a comment:
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I think the file with the path for your FASTQs go after `kmergenie `
Here is the program syntax: kmergenie <read_file> [options]
I wrote this tutorial on how to use it - https://onestopdataanalysis.com/esti...-for-assembly/Last edited by one_stop; 03-07-2020, 09:58 PM.Leave a comment:
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Running kmergenie
Hello every one.
I'm new on bioinformatics. So, sorry if my question is too basic.
I'm trying to run kmergenie. It hasn't worked when I use reads_file.txt with the files I want to calculate the best k-mer. That's what I'm trying:
$ nano reads_file.txt
-> Paste:
../47G_mapped_1_val_1.fq
../47G_mapped_2_val_2.fq
$ kmergenie -l 21 -k 51 -s 5 reads_file.txt -o 47G_kmergenie
The message is:
running histogram estimation
File reads_file.txt starts with character ".", hence is interpreted as a list of file names
Reading 2 read files
End then it stops.
The only way kmergenie has worked is running one file at the time, but as I have paired end reads it's gonna take too long to finish the work.
Please can anybody help me?
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