Hello May I know what is the difference between --input-format PairedEndFastqManifestPhred64 and --input-format PairedEndFastqManifestPhred33 and CasavaOneEightSingleLanePerSampleDirFmt, Is it about sequencing device that has been used for sequencing? I always use --input-format PairedEndFastqManif…

Hi @Fatemah , Great question! [image] Fatemah: what is the difference between --input-format PairedEndFastqManifestPhred64 and --input-format PairedEndFastqManifestPhred33 and CasavaOneEightSingleLanePerSampleDirFmt The Phred variations are explained well here . The difference between manife…

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