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

Question

[bird77]

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?

Answer 1

[lakhujanivijay]

a list of some well known and validated tools

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

check out this paper also.

[bird77]

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

[lakhujanivijay]

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