Does someone have assembled short reads obtained from shotgun sequencing (Proton sequencer) of complex microbial communities? Which is the best tool for assembly of these reads (not-paired-end)? Are the results obtained from assembly of good quality (in term of N50)?
There are too many variables for one to predict what you can expect in terms of N50, e.g. the DNA quality, the complexity of the microbiome in the environment you are sampling, the dynamic range of species, etc. I suggest you try MetAMOS for an assembly (Treangen et al., Genome Biology 14:R2. 2013), it will at least help you get a handle on the contribution of all of these variables.
http://genomebiology.com/content/14/1/R2
Also, I think you should try the pipeline described in this paper, if you have two samples: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes, Albertsen et al.
It was designed for mate-pair or paired-end libraries, but worked well at some point with my 454 non-paired-end reads of cyanobacterial metagenome.
Stefano - we just acquired a Proton in our lab and plan to do a year long metagenomic survey of environmental samples collected weekly. Prior to purchasing the Proton - I could not find much of anyone doing metagenomics on a Proton (the platform is too new; probably there are some pubs in prep - but not out yet). It will be interesting to see how it pans out. Feel free to drop me a message in a few months to see how we're doing…
BTW -- what sort of metagenomics samples are looking at on your Proton?
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools