Bac ends profiling to a genome

[Danil S.]

Hi,

I am looking for the pipeline which provides bac-ends profiling to the reference genome.

I used to work with illumina myseq 16s rRNA paired-end sequences.And i used qiime2 to treat it. Now i have a sanger bac-end library of the whole genome and i need to map them to a genome sequence in order to be able to choose BAC with gene of interest.

I suppose that what i have to do is:

1.Filter out sequences that are 95% similarity or more to each other.

2.Remoove sequences which contain repeats.

3.Map remaining paired sequences.

4.Leave paires of bac-ends with unique hits only.

Thus i can choose a BAC which contains gene of interest for the further research. In theory.

Can anyone suggest tools for this work and maybe correct my "pipeline"?


Thank you!

[GenoMax]

Cross-posted and answered on Biostars: https://www.biostars.org/p/424091/