merging read pair mates using a reference sequence

OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

MIT License

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merging read pair mates using a reference sequence #582

Open mmokrejs opened 1 month ago

mmokrejs commented 1 month ago

Hi, I lack possibility to merge mates (from amplicon sequencing) of a pair using alignment info to a reference. Ideally if they do NOT overlap to fill in the space with Ns. If they overlap, resolve the conflicts using QUAL values (is already implemented in fastp).

Current implementation is described here: https://github.com/OpenGene/fastp/issues/31 Thank you,