Good reference-based genome assembly tool

Question

[traditionalGuy]

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.

[lieven.sterck]

reference based transcriptome or genome assembly?

[traditionalGuy]

Reference based genome assembly. Have edited the title. Thanks

[lieven.sterck]

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.

[traditionalGuy]

Illumina around 300bp

[GenoMax]

See: Reference based assembly

https://www.sciencedirect.com/science/article/pii/S1672022918304376

Answer 1

[Mensur Dlakic]

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.

[h.mon]

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.