Assemble a segment of genome denovo

Question

[cg]

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

[VHahaut]

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

Answer 1

[rtliu]

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