Merged unsync fastq files

[ekar...@gmail.com]

Dear Torognes,

Thank you for updating and maintaining the repository.

I have a question regarding merging un-sync fastq files. During the pre-processing step outside the Vserach pipeline, the order of raw reads in R1 and R2 has changed, and consequently, they are no longer in the same order. 

Does the merge command look at the fastq header before merging, or alternatively, does the pipeline merge them based on min overlaps, max diff etc., that we feed in to command independent of the fastq headers?

Thank you un advance

[Torbjørn Rognes]

Hi

Unfortunately, vsearch requires the R1 and R2 files to be in sync for merging.

- Torbjørn

[Colin J Brislawn]

Good afternoon,

You may have found this already, but just in case, I've use repair.sh from the BB Tools package to re-sync fastq files.

https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/repair-guide/ 

Just like vsearch, you can install bbtools / bbmap with conda:

https://anaconda.org/bioconda/bbmap 

Colin

[ekar...@gmail.com]

Thank you, Torbjørn and Colin.