How to produce a consensus genome
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4.0 years ago
eennadi • 0

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

Assembly sequencing next-gen genome sequence • 1.3k views
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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".

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  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.
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Am so sorry for using Caps

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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.

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Velvet has 2 steps - velveth and velvetg.

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