Question: Quality Of Assembly Based On Ion Torrent Data (Microbial Genome)
2
gravatar for justinhaselbach
6.1 years ago by
United States
justinhaselbach250 wrote:

Hi there. New to Bioinformatics !

Results are as follows: Ion-Torrent Data for a 5 Mbp microbial genome: Aquired 3, 435, 101 high-quality filtered reads, average read length of 180 bp, assembled using MIRA/ CLC Assembler, & got: 350 Contigs (> 500 bp CO), mean contig size: 17 kbp, 110 X Coverage; N50 Contigs: 32 kbp, largest scaffold: 89 kbp, 6000 ORFS/CDSs.

What looks unreasonable/ unacceptable/ gross ? Please feel free to advice and comment ! Just wish to check out and find flaws.

Thanks, Justin

bacteria 454 mira coverage • 2.3k views
ADD COMMENTlink written 6.1 years ago by justinhaselbach250

Really depends on what you are trying to achieve with your data.

ADD REPLYlink written 6.1 years ago by Biomonika (Noolean)3.1k

To Publish a Draft Genome ! In that case ? Thanks,

ADD REPLYlink written 6.1 years ago by justinhaselbach250

If you have time, I would do two more things: 1) reduced coverage, as assembly software might have problem (and often has problem) with as high coverage asi 110X - I would downsample it to let's say one half (55X). Maybe you get better results with less reads:)) 2) I would try also another assembler, such as Trinity and compared number of contigs (maybe even checked how much they differ?). From my experience, MIRA gave me assembly which was very different to one produced by Trinity, so it's worth a try. Good luck :-)

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Biomonika (Noolean)3.1k

Wow ! Thanks a loads ! Worth trying Trinity with half-the-coverage ! Will do so. Thanks again.

ADD REPLYlink written 6.1 years ago by justinhaselbach250
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