Assembler:SOAPdenovo

[mgbfx9]

Hello everyone,

I am newbie. I am working on de novo assembly of human genome.
I am new in the field, but not getting any help. So I would appreciate any sort of help to proceed.

I made the DNA library, and I got my sequencing data from the sequencing facility. They ran my samples on Illumina MiSeq 2x250. This is a 250 bp PE MiSeq multiplex run. I have 4 samples, paired end reads, each has R1 and R2.

I checked the quality by running on FastQC. I chose to run SOAP de novo now, and from the literature I found out that I don't need to trim the edges, or all the preliminary things before assembly, as SOAP de novo has all the tools. I downloaded SOAP de novo assembler, but please help me to start to use it.

Thanks,

[pmiguel]

A MiSeq run will not produce enough data to allow you to do a de novo assembly. You should probably run Bowtie2 or some other mapping engine instead to map your reads to a human reference genome.

--
Phillip

[mgbfx9]

Assembler:SOAPdenovo

Thank you, Phillip.for your suggestion.

I have haploid genome for sequencing. You said that I won't have enough data to do de novo assembly. May I ask you how much data do I need to do de novo assembly? I have more than 5 GB data. Could you please let me know?

Thanks,
mgbfx9

[pmiguel]

I would think 20-30X, at a minimum, for a de novo assembly. So for a human, 60 billion bases. Below that, you would almost certainly get more usable results by mapping your reads to the reference human genome sequence.

--
Phillip