best k-mer(s) to use for Mi seq and Hi seq data
1
0
Entering edit mode
4.3 years ago
Bioinfo ▴ 20

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 • 1.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Ahhh , Thank you :D

ADD REPLY
0
Entering edit mode

and how can i determine K mer using unicycler

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.3 years ago
h.mon 35k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2990 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6