Programs to filter out the Mitochonrial DNA from Hightroughput Sequencing Reads

[fcr]

Hi all,

I have Whole Genome Shotgun Reads (Illumina) of a mammalian species. I am interested in filtering out all the reads matching mitochondrial DNA before starting the downstream analysis. I know the right thing is to blast them or map them against mtDNA. But, Do anyone knows about available software or scripts to do this? I would like to know if there are tools for it before writing the code myself.

Cheers,
Fernando

[peromhc]

Although I have not tried this very approach, I bet you can use Bowtie combined with the --un feature.. Make a fasta file that contains your mt genome, build the bowtie index, and run.

[swbarnes2]

Align to the whole genome, including mtDNA, using bowtie or bwa or whatever. Then you can filter your .bam for reads that align to the mtDNA.

[husamia]

Align to the whole genome, including mtDNA, using bowtie or bwa or whatever. Then you can filter your .bam for reads that align to the mtDNA.

I agree. there is no way to know which reads at mt so you have to align first.

[mjp]

You could build indices with your mapping program of choice and map your reads to it.

Take a look at http://www.ncbi.nlm.nih.gov/genomes/...2759&hopt=html (Organelle Genome Resources) to download sequences for your indices.

Hope it helps.

[SES]

Hi all,

I have Whole Genome Shotgun Reads (Illumina) of a mammalian species. I am interested in filtering out all the reads matching mitochondrial DNA before starting the downstream analysis. I know the right thing is to blast them or map them against mtDNA. But, Do anyone knows about available software or scripts to do this? I would like to know if there are tools for it before writing the code myself.

Cheers,
Fernando

As a sanity check, be sure to BLAST the mtDNA against the genome after you have mapped or assembled your reads. The bowtie --un method is very fast for filtering reads, but unfortunately it does not work in my experience. Sure, it will filter out some reads but when you BLAST your assembly against the organelle genome after assembly it is quite clear that this type of filtering is not really effective.

It is slower, but I use BLAST for filtering, which leaves no contamination in the final assembly. Either way you choose to go, just keep in mind that checking that the filtering actually worked is quick and easy, and will reduce headaches downstream.