Removing host sequences

[tuija]

I am doing NGS on DNA from pig tissues to detect possible microbes in such samples. To reduce the amount of sequences (Ion Torrent) to be analyzed I would like to get rid of all possible pig sequences. Currently I am using Galaxy Bowtie, with the pig genome as reference. However, the amount of unmapped (within these I am expecting to have the microbial sequences that I am interested in) sequences remains high. Would there be another tool to efficiently remove the pig genomic sequences?

Thanks for any comment!

[krobison]

BWA or TMAP would be more appropriate aligners for Ion Torrent data than Bowtie, as they are more tolerant of the higher indel rate (vs. Illumina data). You could either run them alone, or just run them on the fraction not aligning using Bowtie (Bowtie tends to be faster).

[tuija]

Finally I did map to pig genome by Bowtie and continued with the unmapped reads trying different tools includidng TMPA, BWA, Bowtie and Blast using micorobial library as reference. The most reliable was BWA and Blast.

[aarodriguezm]

I am doing NGS on DNA from pig tissues to detect possible microbes in such samples. To reduce the amount of sequences (Ion Torrent) to be analyzed I would like to get rid of all possible pig sequences. Currently I am using Galaxy Bowtie, with the pig genome as reference. However, the amount of unmapped (within these I am expecting to have the microbial sequences that I am interested in) sequences remains high. Would there be another tool to efficiently remove the pig genomic sequences?

Thanks for any comment!

Hi
I have some questions rather than answers for you, sorry
How deep did you have to sequence teh pig genome? and after removing the DNA pig sequences did you obtaine enough microbes sequences?
I mostly work with Human samples, but I`m very interested in some kind of methode to remove host DNA before library preparation. Do you know some?
Thanks

[tuija]

Hi, In this case I specifically took a look on viral sequences. Before DNA extraction did a DNaseI and Benzonase treatment to get rid of lots of genomic DNA while viral nucleic acid is protected within the capside. For RNA samples I did an additional rRNA removal which improved the results a lot.