single eukaryote whole genome de novo assembly

[httzsn]

Hi everyone

I am doing single cell genomics. However, I am a newbies on bioinformatics.

My sample is single picoeukaryotes from the ocean. I did MDA followed by NGS using Hiseq 2500 PE 150 bp with Nextera libraries preparation.

Here, my questions is
1) In order to get better assemblies, which trimming tool do you recommend for trim sequences?

2) For single eukaryotes do novo assembly, I did not find suitable assemblers.
Could you recommend some for me? P.S. I tried several assemblers, like, IDBA_UD, SPADes, however, I can't get long contigs, N50 only around 1500bp.

3) Could you recommend some experts or research center who are professional on de novo assembley?

4) BTW, the genome size of my sample is around 20 Mbp to 40 Mbp according to reference paper.

All my PhD project is stuck here, I wish you could help me out.
Thank you very much!

Cheers

[chariko]

Regarding your questions:

1) If you want to trim your sequences (actually I do not recommend it at all) you could use prinseq (http://prinseq.sourceforge.net/) which actually works very well and it is easy to use.

2) I would recommend you to use MIRA assembler followed by manual curation with gap5. This will allow you to control in every moment the contigs you are joining.

At least I would recommend having enough coverage to get good results.

[Brian Bushnell]

What kind of coverage do you have, and what's your insert size distribution? Also, posting FastQC results is often helpful.

Sometimes normalization can be quite useful with MDA'd single cells prior to assembly.