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You're here because you have linked-read data and might want to convert it between different linked-read formats. Many of the conversions available in Djinn work for either FASTQ or BAM files. Djinn also includes other tools for e.g. extracting barcodes from linked-read data, sorting by barcodes, etc. Nifty convenience things.

Convert files

Djinn converts between linked-read data formats. It supports:

• 10X
• haplotagging
• stLFR
• TELLseq
• standard

You can convert between these formats in terms of FASTQ type or barcode style.

NCBI submission

NCBI strips out sequence headers from FASTQ submissions, so it would be best to convert your linked-read FASTQ data into an unaligned BAM file, with the linked-read barcode stored in the BX or BC tag. Djinn provides a convenience function to convert to (or from) this format, although we make no effort to hide the fact it's just one-liner samtools commands.