Hello all,
I am using cloudbrush de-novo assembler in order to perform assembly on illumina reads from gardenia (plant). Following the same process which is successful for assembling E. Coli raw reads, it fails when I try to assemble on gardenia as I describe here (no useful debugging info).
Thus I was wondering if the procedure of de novo assembly from plants' raw reads differentiates from other organisms, in such a way that an assembler could fail in one case and succeed in the other.
Any thoughts?
2 answers
The data set you are trying to assemble (http://www.ncbi.nlm.nih.gov/sra/SRR1045129) is transcriptomic (RNA-Seq) data. You can not use this data for genome assembly.
Most likely you've hit memory limit. Plant genomes are different in that they are much larger than bacterial ones (compare ~4.5Gbp of gardenia vs ~4.5Mbp of E.Coli).
•
written
by
lomereiter
Log in to answer this question.
-
What are your preferred programs for processing DNA long reads? (de novo assembly)
written by ExtentHonest56 •
-
Is it normal for RCorrector to remove millions of reads?
written by nina.maryn •
-
What short read assemblers are appropriate for a tuberculosis paired fastqs coming from SRA?
written by conifer_genomics_uk •
-
How to accurately identify the centromere sequence of a species from draft assembly or raw reads?
written by bampress •
-
Need tools recommendation for plant RNAseq data
written by bioinforesearchquestions
-
Do we have any other de novo assembly approaches than Graph based (OLC and De bruijn), Seed Extensi…
written by saranpons3
-
Why less number of hadoop/spark based de novo assemblers?
written by saranpons3
-
BAC sequencing issues
written by int11ap1
-
Merge 2 de novo assembly generated using Trinity?
written by nbvasani
-
A Question About Hybrid/Mix -Genome Assembly
written by Lhl
