K-mer selection for correcting long reads with short reads
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4 months ago
zack.saud ▴ 50

Hi all,

Hybrid long read error correction tools such as FMLRC and Ratatosk allow the user to set k-mer pass lengths as part of the parameter selection. If I have 150 bp Illumina reads and want to correct nanopore reads, what are the best short and long k-mer lengths to choose? Are there any tools that can help calculate optimal values for hybrid corrections tools? If it needs to be determined empirically, can anyone share their experience of the best values to set for 150 bp Illumina reads?

Many thanks in advance

Bionformatics • 171 views
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Entering edit mode
4 months ago
zack.saud ▴ 50

Hoping it is not a problem if I bump this post

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