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

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

sequence assembly alignment sequencing
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updated by h.mon h.mon • written by Bioinfo • Bioinfo

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

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written by cschu181 cschu181

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

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written by Bioinfo • Bioinfo

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.

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written by cschu181 cschu181

and how can i determine K mer using unicycler

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written by Bioinfo • Bioinfo

1 answer

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.

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written by h.mon h.mon

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