merging paired ends illumina reads without quality with Pear

Question

[Lapsus]

Hi to everyone, I got some environmental metagenomes. I would like to merge the pair reads (forward and reverse), which are already denoised, and not anymore in fastq format but in fasta. Looking around seems that all the tools which carry out this task, such as Pear, need as input fastq reads. There are some tools like reformat of BBmap, which could allow me to reformat fasta to fastq cheating on the quality.

Thus, what I was thinking to do is: reformat all reads with reformat.sh, the merge the pairs with Pear using different parameters which could be affected by the fake quality, such as: changing the scoring method (-e) from Assembly score (AS). Use +1 for match and -1 for mismatch multiplied by base quality scores ( the default one) to: Ignore quality scores and use +1 for a match and -1 for a mismatch. Obviously use a quality score threshold which lower than the fake one. But I don't know if this method is right or wrong.

I really thanks in advance who will help me!

Answer 1

[GenoMax]

bbmerge.sh may work though I have not tested it with fasta files.

[Lapsus]

You are right!

$ bbmerge.sh --help [.......] Input may be stdin or a file, fasta or fastq, raw or gzipped. [......]

PS: it was not written in the online guide, for that I have opened this post!!!

Thanks for the suggestion!