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  • Assembling single genomen from metagenome with reference

    Hi seqanswers,

    Can anyone recommend an assembler for generating a single draft genome from a metagenome (Illumina 2500 pe reads) when a fairly good reference for the genome of interest is available?

    My current approach is to do a denovo assembly using SPades and then rearrange the contigs against the reference using MAUVE, was wondering if there were any other options out there?

    Cheers
    N

  • #2
    And on a related note, what would be the best way to drop contigs that don't align to the reference?

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    • #3
      Have come up with another way - map pre-assembled contigs using ABACUS/Contiguator which automatically drops non-aligned contigs .

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