Question: Assemble a segment of genome denovo
0
gravatar for cg
3.4 years ago by
cg10
United States
cg10 wrote:

Hello 

I am trying to find a tool that helps assemble a genome segment from a fastq file, without mapping to a reference genome. I do have the reference genome, but I am checking for diversity between two genomes (specifically indels, MITES etc.) .

As per my understanding, If I assemble the genome denovo and align fasta file, I will lose that information I am looking for as an assembler might filter the repetitive regions. 

Any pointers to this will be of great help.

 

Thank you. 

  

ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 3.4 years ago by cg10

You could try to use velvet (http://genome.cshlp.org/content/18/5/821.full) if you have short reads.

ADD REPLYlink written 3.4 years ago by VHahaut1.1k
0
gravatar for rtliu
3.4 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

You may try Cortex, reference Cortex paper

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph

 

ADD COMMENTlink written 3.4 years ago by rtliu2.0k
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