Modify and convert linked-read FASTQ and BAM files

Extract barcodes

Get all the barcodes from the input file(s)

Sort by barcode

Sort records by barcode rather than name or position

Filtering

• separate linked reads from singletons
• omit invalid barcodes

Convert files

Djinn converts between linked-read data formats. You can convert between formats in terms of FASTQ type or barcode style. It supports:

• 10X
• haplotagging
• stLFR
• TELLseq
• standard

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 it's really just a basic samtools command.

Hi-C spoofing

This is extremely experimental and it converts a paired-end linked-read fastq file pair into one that conforms to Hi-C expectations by mix-matching the R1s and R2s of reads that share a barcode.