The best k mer to use for illumina data

Question

[Bioinfo]

Hello everyone . i hope you and your family and friends are doing fine

Please i have a question about K mer can anyone please tell me simple definition of k mer and it's important in assemblage and what is the best k mer to use for Hi seqdata (Length of the reads = 50 ) only and Mi seq Data ( length of the reads = 50 ) only and both Mi seq and Hi seq data . because in some samples (bateria strains ) i have both Hi seq data and Mi seq data , but in other samples i have just Mi seq data and Hi seq for others

Thank you very much

[GenoMax]

Depending on the program you are going to use for the assembly, the program will try a range of k-mers out and select the best one. For some programs you will need to make a selection and try a few out. You can also use programs like kmergenie to estimate these.

This thread also has some information: best kmer for genome size estimation

[Bioinfo]

Thank you very much for your answer , I'm using shovill for the assembly please tel me what things i should take in consideration to choose the best k-mer ( i just know , the number of contigs and N50 ) are they enough

[Mehmet]

you can use this tool to see K-mer distribution in your data.

jellyfish

Answer 1

[h.mon]

Shovill, by default, use SPAdes as the underlying assembler, and SPAdes:

1. automatically chooses the best kmer lengths based on read length.
2. is a multi-kmer assembler, which means it uses several kmer lengths during the assembly process.