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Which is the best input file for denovo assembly with Illumina paired data: Fastq, Fasta or Fasta interlaced ?

Hi, I am doing denovo assembly on Illumina paired reads with SOAPdenovo2. It allows fastq, fasta, fasta interlaced and bam files. I am now trying and assembly with the first three ones at the same time and it's taking a long time. I wonder if it might be redundant to put all this information. In case it is, which one should I use to get the best result?

Thanks!!!

assembly
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written by minesrebollo • minesrebollo

Are those three the same data in different formats or different data in different formats?

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written by GenoMax GenoMax

In that case it's not a good idea to put in the same data more than once.

Fastq is the most common format for Illumina paired-end data, and it has the quality values in case the assembly software makes use of the base qualities.

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written by mastal511 mastal511

So, maybe I shouldn't trust this assembly and run another with just the fastq files? Thanks a lot!!

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written by minesrebollo • minesrebollo

That would be the wise thing to do.

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written by GenoMax GenoMax

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