#66 Stitching read pair R1 andf R2 sequences based on alignment from SAM/BAM

[Martin Mokrejs]

Hi Brian,
there are many tools (bbmerge.sh from BBmap, NGmerge, VSEARCH, USEARCH, ...) which can look for some overlap between members of a FASTA/Q read pair but is there a tool which can use already mapped pair members to their common reference and just merge them, evtl. insert the needed Ns as a linker in between with proper length? I have the .fastq.gz files still around so it could maybe just act on position-sorted SAM/BAM and poke through the synced read pairs in R1 and R2 files and merge them accordingly (replace Ns with a nucleotide from the other mate, eventually prefer higher QUAL)?

https://sourceforge.net/projects/bbmap/
https://drive5.com/usearch/manual/merge_pair.html
https://github.com/jsh58/NGmerge
https://cme.h-its.org/exelixis/web/software/pear/