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  • Assemblers for Short Reads

    I want to use an assembler to assemble the unmapped illumina reads from an alignment to S288C (yeast genome). So far I have been using SSAKE and it seems to be working fine, but I would like to compare the results of SSAKE to another assembler. Are there better/other assemblers out there that would be worth trying? Thanks for your time, sorry if this is a repost.

  • #2
    You can see some comparative benchmarks of current assemblers here:

    continuous, objective and reproducible evaluation of genome assemblers using docker containers


    SSAKE is not included, though. I commonly use both Spades and Velvet.

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    • #3
      Thanks this is what I was looking for.

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