Mapping amplicon to a reference sequence with iteration / elongation

Question

[marion.couedel]

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

[mmahe]

Hi,

I have seen that your post is old, but I have the same issue than you. Do you remember the solution you found?

Thank you.

Answer 1

[marion.couedel]

Hi, Finally, I solve my problem with several customs scripts.

[GenoMax]

Your problem description is not clearly stated. I have tried to read it a few times but can't figure out exactly what you want/need to do. Since your custom scripts are not going to be available to people who find this thread in future if you are able to provide a step-wise logical description of what your scripts are doing perhaps an alternate solution can be found.