Question: abyss-pe genome assembly
0
gravatar for Igor Lalin
5 weeks ago by
Igor Lalin0
Canada/London/London Research and Development Centre
Igor Lalin0 wrote:

I discovered something interesting and it could be a fact that has been known for some time regarding Konnector:

When running the following command after qlogin:

 konnector -j 40 -k 96 -o kon96 out_reads_1.fastq out_reads_2.fastq

Konnector produces: kon96_reads1.fq, kon96_reads2.fq and kon96_pseudoreads.fa

If running konnector as a shell script it will not produce kon96_pseudoreads.fa but kon96_merged.fa.

This is an important difference because Konnector reads can be fed into Abyss-pe for finishing the genome assembly.

tool abyss-pe konnector • 127 views
ADD COMMENTlink modified 5 weeks ago by lieven.sterck4.1k • written 5 weeks ago by Igor Lalin0
2

Contact the team at BCGSC directly: https://github.com/bcgsc Their members are infrequent users here.

ADD REPLYlink written 5 weeks ago by Kevin Blighe39k
2

or open an issue on the abyss github page

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lieven.sterck4.1k
1

Hi Igor Lalin ,

I also edited you post title category, (from Tool to Question) as this is not really a tool announcement (for which we reserve that specific tag) but rather a question about a tool.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lieven.sterck4.1k
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