Using QIIME2 with BBmerge


I normally import my sequencing data as follows:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path MANIFEST.csv
--output-path 1SampleDataPaired.qza
--source-format PairedEndFastqManifestPhred33

However, I now want to join my forward and reverse sequences together with BBmerge before using QIIME2. I successfully merged each pair into one fastq file, but now I do not know how to import the files.

I tried this:

qiime tools import
--type 'SampleData[JoinedSequencesWithQuality]'
--input-path /path/to/directory/
--output-path 1SampleData.qza \

But it's not working:

Missing one or more files for SingleLanePerSampleSingleEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

What do you suggest? Thanks.

You can still use the manifest format to import your joined reads, update your first import command above to type SampleData[JoinedSequencesWithQuality] and you should be good to go.

1 Like

Thanks, though you forgot to mention I must also change --source-format to [SingleEndFastqManifestPhred33]

qiime tools import --type 'SampleData[JoinedSequencesWithQuality]' --input-path MANIFEST.csv --output-path 1SampleDataPaired.qza --source-format SingleEndFastqManifestPhred33

The manifest file also was changed, for one line per file with direction "forward" for all. I didn't realize I still needed the "direction" column, which threw me off.

Thanks for the help!

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