Hi everyone,
I am trying to assemble a bacterial genome using PacBio reads and short illumina reads from a metagenomic pool of both eurkaryotic host and bacterial sequences.
In an ideal world, I would have been able to culture the bacteria and obtain pure DNA to sequence and assemble from, but its cultivation has proved challenging. So, instead we have a ton of metagenomic data sequenced obtained from whole host DNA. We have roughly ~70 million Illumina MiSeq paired end reads (2x150) and ~120,000 PacBio reads (5-20 KB). I suspect that I have roughly 3x coverage of the bacterial genome with the PacBio reads and ~20-30x coverage with the illumina reads (with 80-90% of the reads likely being host). This project is further complicated by the fact that the host genome is not fully sequenced, so I cannot remove known host sequence to simplify analysis and de novo assembly.
Could anyone recommend an appropriate set of programs/pipeline in order to isolate and assemble the bacterial genome? Thanks so much!
I am trying to assemble a bacterial genome using PacBio reads and short illumina reads from a metagenomic pool of both eurkaryotic host and bacterial sequences.
In an ideal world, I would have been able to culture the bacteria and obtain pure DNA to sequence and assemble from, but its cultivation has proved challenging. So, instead we have a ton of metagenomic data sequenced obtained from whole host DNA. We have roughly ~70 million Illumina MiSeq paired end reads (2x150) and ~120,000 PacBio reads (5-20 KB). I suspect that I have roughly 3x coverage of the bacterial genome with the PacBio reads and ~20-30x coverage with the illumina reads (with 80-90% of the reads likely being host). This project is further complicated by the fact that the host genome is not fully sequenced, so I cannot remove known host sequence to simplify analysis and de novo assembly.
Could anyone recommend an appropriate set of programs/pipeline in order to isolate and assemble the bacterial genome? Thanks so much!
Comment