How to produce a consensus genome

Question

[eennadi]

I have two sequences I wish to assemble to give a consensus genome. I am using Velvet assembler

would this command line be OK

./velveth conref_out 35 -fastq.gz -shortPaired -separate \
    /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/EN28FP.fq.gz \
    //Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/EN28RP.fq.gz \
    /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/KN99aFP.fq.gz \
    /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/KN99aRP.fq.gz

where
FP= forward paired
RP= Reverse paired
EN28= Sequence 1
KN99a= Sequence 2

Thanks

[Istvan Albert]

An assembler like velvet does already produce a "consensus" genome. But I suspect you mean something else by the word "consensus" than what velvet does. So it would be better to clarify what you mean by "consensus".

[Ram]

1. Do not use all caps in your post (or in the post title) - it is rude
2. Try the command and test the output. If it doesn't match your expectations and you are unable to figure out why, ask us then, and give us specifics.

[eennadi]

Am so sorry for using Caps

[Joe]

If you mean you just want to build a single genome but from 2 sets of input reads, you can simply cat The R1 files together, and then do the same for the R2, and run your assembler on the “uber” reads.

[mastal511]

Velvet has 2 steps - velveth and velvetg.