Assembly_velvet

[pic79]

Hi there,

I am currently working with illumina data. I have three different lanes.
the first lane yielded a paired reads file while the other two are single end reads.
I was thinking to assemble the reads with velvet firstly and then compare with other assembler tools.

How do I go about it? what's the step to assemble the three lines?

Thanks

[vishnuamaram]

Hi pic79,

Are the three lanes consist of data of same sample.

(1) What is your data mainly. DNA,RNA, small RNA.
(2) Which organism
(3) Consider all options of having a reference genome available or not.

Then you should think of assembly or analysis.

You can concatenate data of three lines or if you have sam/bam files you may use samtools merge option.

[pic79]

assembly velvet

Hi vishnuamaram,

thank you for your reply.

My data are cDNA from a gasteropod and (3) no a reference genome



Thanks

[mastal]

You can combine the three lanes of data with velvet, using the parameters -shortPaired -separate for the paired end reads and -short for the single end reads.

velveth ...... -shortPaired -separate lane1_R1.fastq lane1_R2.fastq -short lane2.fastq lane3.fastq

See the velvet manual.