best k-mer(s) to use for Mi seq and Hi seq data

Question

[Bioinfo]

Hello everyone i hope you're doing well

i want to assemble three kind of data using spades first one is Mi seq data where length of reads is 200 b and Hi seq data where the length is 50 and the third file is contain the two data ( Hiseq and Miseq)

my question is what is the best k mers to use to asemble each one of these data and what is the character that i should analyse to determine the best assembly

Thank you very much

[cschu181]

If that is genomic data you could use unicycler (which wraps spades) to let it determine the best k-mer value.

[Bioinfo]

but i'm using another software (shovill) which wraps spades too

[cschu181]

Doesn't do you much good to determine the k-value, though, does it? :D Could run unicycler, let it determine the k, then run shovill with that k if you must.

[Bioinfo]

Ahhh , Thank you :D

[Bioinfo]

and how can i determine K mer using unicycler

[GenoMax]

Please don't ask same/similar questions in new threads. You had already asked this question here: The best k mer to use for illumina data

Answer 1

[h.mon]

Why bother choosing kmer lengths, if the default setting is automatic selection of appropriate kmer lengths? From the shovill help:

--kmers XXX     K-mers to use <blank=AUTO> (default: '')

Besides, if the coverage of one of the data sets is good enough (~50-100x), you can use just this data set for the assembly.