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Good reference-based genome assembly tool

SPAdes has "trusted contigs" option, but it's not really reference-based assembly. I know velvet has that option, but I don't find it user-friendly. Is there any other reliable tool for reference-based assembly.

assembly assembly sequencing genome
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updated by Mensur Dlakic Mensur Dlakic • written by traditionalGuy • traditionalGuy

reference based transcriptome or genome assembly?

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written by lieven.sterck lieven.sterck

Reference based genome assembly. Have edited the title. Thanks

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written by traditionalGuy • traditionalGuy

not sure what kind of data you are working with (short read? long read?) but if memory serves I thought that Flye assembler could also do (some sort of) reference based.

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written by lieven.sterck lieven.sterck

1 answer

For small genomes (< 40 Mb), MIRA works very well. Beware that it can do a hybrid assembly using data from different technologies, excluding PacBio and Nanopore.

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written by Mensur Dlakic Mensur Dlakic

Actually, MIRA can use PacBio and Nanopore reads, provided:

  • the reads have been error-corrected (either PacBio circular consensus, or Illumina-correction for both PacBio and Nanopore),
  • in case the reads are really long, they need do be chopped to a 32kb maximum length, probably even less, so that memory usage doesn't explode.

MIRA is a great assembler, but overly complex, and development apparently stopped at 2016, so it didn't catch up with the latest sequencing technologies improvements.

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written by h.mon h.mon

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