Fwd: installing with higher kmer

[Brian Mailloux]

Hello, I am running transabyss on a cluster with sun grid engine (I use qsub). I installed with conda and bioconda and I am up and running.  However  I wanted to use larger kmers but I can't as it seems like the kmer cutoff is 65.  I was wondering if there is an option with using conda to increase the kmax when installing with conda.  Or do I need to recompile?  And as I am a total novice is there an easy way to recompile on the cluster?   Thank you for the help! Sincerely, Brian  

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Brian J. Mailloux, PhD
Associate Professor

Department of Environmental Science
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[Ka Ming Nip]

Hi Brian,

Using large kmer sizes for transcriptome assembly is not recommended.

To use larger kmers in ABySS (versions 2.0.x), you can recompile ABySS manually:

./configure --enable-maxk=​96

make

Hope that helps!

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab
Canada's Michael Smith Genome Sciences Centre

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From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Brian Mailloux <bmai...@barnard.edu>
Sent: June 15, 2020 9:32 AM
To: trans...@googlegroups.com
Subject: Fwd: installing with higher kmer

 

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[Brian Mailloux]

Ka Ming, Thank you. I was copying a paper where they are assembling ribosomal RNA and used kmer from 61-101 in 4 unit steps.  I was doing a parallel analysis and trying to copy their method.   I am happy to use smaller kmer values.  I figured I could do 33-61.  I will try that first before compiling.  Regards, Brian

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