Hi, I try to reconstruct a sequence of 700 bp (barcode) with 250x pair-end Illumina reads.
I have several barcodes which are multiplexed in an Illumina Index file. Each final barcode have a length of 700bp. For the sequencing needs, each barcode was aleatory cut. After sequencing, I juste know the tag+primer nucleotide sequences, which permit to find the beginning of my barcode (250bp). Then I would like map all the reads of my Index file to this beginning read.
I currently work with Geneious Prime, which permit to do : "Map to reference with iteration" It's work great, but take a lot of time to do it manually.
Have you an idea of how i can do that ? The only solution, I have found, is to use minimap 2 and export the consensus alignment from sam files to fasta, and do it again until my consensus > 700bp Thanks