alekseyzimin
commented
4 years ago Hi, sorry for delayed reply. The most cost effective library is 2x150 with 400-500 bp fragment size. 2x250 will work slightly better but will cost a lot more.
On Wed, Nov 27, 2019 at 2:51 AM Marios Gavrielatos notifications@github.com wrote:
Dear @alekseyzimin https://github.com/alekseyzimin, which is the optimal fragment mean size and short-read size of the Illumina paired end reads in order to get the best results in a hybrid assembly using nanopore long-reads? According to https://software.broadinstitute.org/software/discovar/blog/?page_id=375#libcon, we would like to create library fragments of ~400bp, and sequence these fragments with 250 base paired-end reads on an Illumina NovaSeq 6000. This technique will create an overlap between the two reads. Will this help the assembler to create a better final result? Do you suggest something else? Thank you in advance, Marios
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Dear @alekseyzimin, which is the optimal fragment mean size and short-read size of the Illumina paired end reads in order to get the best results in a hybrid assembly using nanopore long-reads? According to https://software.broadinstitute.org/software/discovar/blog/?page_id=375#libcon, we would like to create library fragments of ~400bp, and sequence these fragments with 250 base paired-end reads on an Illumina NovaSeq 6000. This technique will create an overlap between the two reads. Will this help the assembler to create a better final result? Do you suggest something else? Thank you in advance, Marios