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Old 08-20-2019, 06:30 PM   #1
Junior Member
Location: Brazil

Join Date: Aug 2019
Posts: 3
Question 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:


$ 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?
fabio.marcelo is offline   Reply With Quote
Old 03-07-2020, 07:37 PM   #2
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Location: USA

Join Date: Mar 2020
Posts: 2

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 -
Data Scientist and blogger (

Last edited by one_stop; 03-07-2020 at 08:58 PM.
one_stop is offline   Reply With Quote

kmer counting, kmergenie

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