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Tools for assembly of microbial genomes (with and without reference genomes)

I have several microbial genomes sequenced with Illumina MiSeq (probably not larger than 7Mbp).

For some of the genomes, I have reference genomes, for others I don't.

Which tools can I use to perform assembly of microbial genomes with and without reference genomes?

assembly
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updated by lakhujanivijay lakhujanivijay • written by bird77 • bird77

1 answer

a list of some well known and validated tools

  • ABySS
  • SGA
  • SOAPdenovo2 + GapCloser
  • SPAdes
  • Velvet

check out this paper also.

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written by lakhujanivijay lakhujanivijay

Thank you for your answer. Which assembler would you use for reference-based assembly?

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written by bird77 • bird77

Welcome! Upvote or accept as answer if this helped you. Check out this

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written by lakhujanivijay lakhujanivijay

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