https://github.com/pdimens/djinn

Convert linked-read FASTQ/BAM files between formats, almost like magic.
https://github.com/pdimens/djinn

Last synced: 5 months ago
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Convert linked-read FASTQ/BAM files between formats, almost like magic.

• Host: GitHub
• URL: https://github.com/pdimens/djinn
• Owner: pdimens
• License: gpl-3.0
• Created: 2025-09-09T14:51:42.000Z (11 months ago)
• Default Branch: main
• Last Pushed: 2026-02-16T14:46:45.000Z (5 months ago)
• Last Synced: 2026-02-16T22:28:51.541Z (5 months ago)
• Language: Python
• Homepage: https://pdimens.github.io/djinn/
• Size: 3 MB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
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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](https://pdimens.github.io/harpy/getting_started/linked_read_data/#linked-read-data-types)

## 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.