Hi, @aitor.blancomiguez .
I noticed there is an argument “–no-head” in bowtie2 that could clear the headlines startswith “@” character. Can that be used to replace the if not o[0].startswith('@'): in metaphlan(3.0.9).py ~413 line?
Hi @cquxiaoy
The @ headers are needed for the StrainPhlAn pipeline, so we need to keep them in the SAM files
Got it! Thanks. 