Hi,
I am a newbie PhD student and I just started working with Illumina DNA reads (~80 bp). My main experience comes from 454 assemblies (using MIRA, newbler).
I have some doubts about how to use the Illumina reads' information. Basically, I'd like to check the support (using coverage and quality) of the Illumina reads I have (30M+, single end) for each position of my 454 genome, eventually editing the genomic sequence if, let's say, 95% of the reads aligned on a particular position suggest the same mismatch.
Does anybody know if there are tools that make this?
Also, I could use the Illumina reads for a mapping assembly. I never did one, as I never managed to get MIRA not to crash while doing it. Does anybody know if there are tools that not only map short reads on a reference sequence but also INTEGRATE the mapped assembly and the reference one?
I am a little bit lost. Any comment or suggestion is welcome!
I am a newbie PhD student and I just started working with Illumina DNA reads (~80 bp). My main experience comes from 454 assemblies (using MIRA, newbler).
I have some doubts about how to use the Illumina reads' information. Basically, I'd like to check the support (using coverage and quality) of the Illumina reads I have (30M+, single end) for each position of my 454 genome, eventually editing the genomic sequence if, let's say, 95% of the reads aligned on a particular position suggest the same mismatch.
Does anybody know if there are tools that make this?
Also, I could use the Illumina reads for a mapping assembly. I never did one, as I never managed to get MIRA not to crash while doing it. Does anybody know if there are tools that not only map short reads on a reference sequence but also INTEGRATE the mapped assembly and the reference one?
I am a little bit lost. Any comment or suggestion is welcome!
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