How to produce consensus genome

[emmannaemeka]

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

would this commandline 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

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

Thanks

[GenoMax]

For reference cross-posted: https://www.biostars.org/p/284783/