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
1 answer
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
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