Split oxford nanopore MinION fastq file based on barcode
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4.3 years ago
ambi1999 ▴ 50


How can I split a single fastq file into multiple fastq file based on barcode in the header of reads?

I got a single oxford nanopore MinION fastq file containing reads from multiple samples. Each read has a barcode in header identifying the sample. For example as follows.

@7a68bd87-67c2-4478-9a3d-a6b81a624b70 ch=483 read=12720 start_time=2018-05-03T18:18:46Z barcode=BC05 runid=658668ec6593d6d2a9d8f0a666d4bd556e161839

I want to get split the fastq file into smaller fastq files based on the barcode. Is there a way to do that? I can of course write my own script to do that but I am sure there is already a tool for it.

Tried searching poretools but could not find any easy way.

Thx for help, Ambi.

oxford nanopore minion minion fastq barcode split • 2.2k views

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