Question: How can I assembly big genome by abyss with 128 Gb ram
1
gravatar for Mbillah
9 months ago by
Mbillah110
Chittagong
Mbillah110 wrote:

I tried to get 140 million read assembly by abyss-pe, But memory could not load it(sparsehash fatal error). As a result I divided my fastq file and created two contig file (70 million reads). is there any quality problem? and now I want to make this contig file one. how can I do this? Can I continue to work with the combined contig file?

assembly • 330 views
ADD COMMENTlink modified 9 months ago by jean.elbers1.2k • written 9 months ago by Mbillah110
1

I wouldn't divide up the fastq.

Soapdenovo2 might be more memory efficient for you.

Minia certainly will be, but assemblies are poor in my experience.

Good luck.

If you're really struggling and those tools don't work I could perhaps run assemblies for you if you gave me the exact commands to run.

ADD REPLYlink written 9 months ago by colindaven1.6k
2

Although Minia alone really produces too fragmented assemblies, the GATB-Minia-Pipeline results in better assemblies and keep memory usage low.

ADD REPLYlink written 9 months ago by h.mon26k
2
gravatar for jean.elbers
9 months ago by
jean.elbers1.2k
jean.elbers1.2k wrote:

ABySS offers a bloom filter (https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graph), so you could redo the assembly using the bloom filter to reduce memory usage.

ADD COMMENTlink written 9 months ago by jean.elbers1.2k
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